diff --git a/pom.xml b/pom.xml index 67e2d1b78..2c2fa689c 100644 --- a/pom.xml +++ b/pom.xml @@ -173,7 +173,7 @@ ${project.reporting.outputDirectory}/apidocs - ${gatk.basedir}/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help + ${gatk.basedir}/public/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help @@ -198,8 +198,7 @@ ${project.build.outputDirectory} ${project.groupId} - - gatk-tools-public + gatk-utils ${project.version} 2g @@ -689,7 +688,7 @@ false - org.broadinstitute.gatk.utils.help.GATKDoclet + org.broadinstitute.gatk.tools.walkers.help.WalkerDoclet ${project.groupId} gatk-package-distribution diff --git a/protected/gatk-package-distribution/pom.xml b/protected/gatk-package-distribution/pom.xml index ad48250bb..2fd3c3b8f 100644 --- a/protected/gatk-package-distribution/pom.xml +++ b/protected/gatk-package-distribution/pom.xml @@ -43,6 +43,11 @@ gatk-tools-protected ${project.version} + + + org.slf4j + slf4j-log4j12 + samtools @@ -73,7 +78,7 @@ ${project.groupId} - gatk-engine + gatk-utils ${project.version} example-resources tar.bz2 diff --git a/protected/gatk-queue-extensions-distribution/pom.xml b/protected/gatk-queue-extensions-distribution/pom.xml index 7c4035b04..44018ec4e 100644 --- a/protected/gatk-queue-extensions-distribution/pom.xml +++ b/protected/gatk-queue-extensions-distribution/pom.xml @@ -41,6 +41,10 @@ log4j log4j + + picard + picard + ${project.groupId} - gatk-tools-public + gatk-utils ${project.version} test-jar test diff --git a/protected/gatk-queue-package-distribution/pom.xml b/protected/gatk-queue-package-distribution/pom.xml index f3de9c0d9..5a077ef29 100644 --- a/protected/gatk-queue-package-distribution/pom.xml +++ b/protected/gatk-queue-package-distribution/pom.xml @@ -80,7 +80,7 @@ ${project.groupId} - gatk-engine + gatk-utils ${project.version} example-resources tar.bz2 diff --git a/protected/gatk-tools-protected/pom.xml b/protected/gatk-tools-protected/pom.xml index 601939a92..24ceffe87 100644 --- a/protected/gatk-tools-protected/pom.xml +++ b/protected/gatk-tools-protected/pom.xml @@ -48,7 +48,15 @@ ${project.groupId} - gatk-tools-public + gatk-utils + ${project.version} + test-jar + test + + + + ${project.groupId} + gatk-engine ${project.version} test-jar test diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java index d9f59d856..9ad2282ea 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java @@ -49,15 +49,14 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.tools.walkers.bqsr; +package org.broadinstitute.gatk.engine.recalibration; import org.apache.commons.collections.CollectionUtils; import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.commandline.Gatherer; -import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReport; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.broadinstitute.gatk.utils.recalibration.RecalibrationReport; import java.io.File; import java.io.FileNotFoundException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java index 5b342c8be..b524ad08a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.WalkerManager; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java index be64dc4de..9095f695e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import com.google.java.contract.Ensures; import htsjdk.samtools.SAMTag; @@ -58,7 +58,8 @@ import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.utils.recalibration.EventType; +import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.File; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java index c33089449..b01359fca 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java @@ -49,14 +49,14 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java index 001643b07..e054805af 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java @@ -49,9 +49,9 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java index e2aed8b48..c02dd4881 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java @@ -49,10 +49,11 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.LRUCache; +import org.broadinstitute.gatk.utils.recalibration.EventType; /** * The object temporarily held by a read that describes all of it's covariates. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java index 6cfc435f7..c92ef1773 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; /* * Copyright (c) 2009 The Broad Institute diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java index f3759cdb7..14b4c762b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java index 9c5739466..f2f33ee59 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java @@ -49,16 +49,16 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.engine.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.utils.classloader.JVMUtils; -import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.recalibration.EventType; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.R.RScriptExecutor; import org.broadinstitute.gatk.utils.Utils; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java index 4bc4af2e4..1b2129f3d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java @@ -49,15 +49,14 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.tools.walkers.bqsr; +package org.broadinstitute.gatk.engine.recalibration; import com.google.java.contract.Requires; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.*; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.GATKException; -import org.broadinstitute.gatk.utils.recalibration.RecalUtils; import java.io.File; import java.io.PrintStream; @@ -298,7 +297,7 @@ public class RecalibrationArgumentCollection implements Cloneable { * @return never null, but a zero-size collection if there are no differences. */ @Requires("other != null && thisRole != null && otherRole != null && !thisRole.equalsIgnoreCase(otherRole)") - Map compareReportArguments(final RecalibrationArgumentCollection other,final String thisRole, final String otherRole) { + public Map compareReportArguments(final RecalibrationArgumentCollection other,final String thisRole, final String otherRole) { final Map result = new LinkedHashMap<>(15); compareRequestedCovariates(result, other, thisRole, otherRole); compareSimpleReportArgument(result,"no_standard_covs", DO_NOT_USE_STANDARD_COVARIATES, other.DO_NOT_USE_STANDARD_COVARIATES, thisRole, otherRole); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java index a2b83ccb6..a9b401c2b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java @@ -49,16 +49,16 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; -import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.utils.recalibration.EventType; +import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; import java.io.*; import java.util.*; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java index e1c7820a4..ad227f9bd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java @@ -49,11 +49,12 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import com.google.java.contract.Ensures; import org.broadinstitute.gatk.utils.collections.LoggingNestedIntegerArray; -import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.utils.recalibration.EventType; +import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; import java.io.PrintStream; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java index 99264430d..f1ef944dc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java @@ -49,16 +49,16 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.clipping.ClippingRepresentation; import org.broadinstitute.gatk.utils.clipping.ReadClipper; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.ArrayList; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java index a6fddb799..4c984c10b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java @@ -49,10 +49,10 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; -import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /* diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java index 9ef17d89c..627402acb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java @@ -49,10 +49,10 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; -import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.NGSPlatform; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java index 771c49771..c276f43ec 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; /** * [Short one sentence description of this walker] diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java index e31588468..889e00b9a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java @@ -49,10 +49,10 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; -import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java index 9eadcf458..9f4c34463 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java @@ -49,10 +49,10 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java index 1cb4be39c..64b32d766 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java @@ -49,12 +49,12 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.RecalibrationArgumentCollection; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import org.broadinstitute.gatk.utils.BaseUtils; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java index 398633062..fb6aeaf85 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java index 345ef0d7d..10a7f6672 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java index b1b0ca457..d961b1460 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; /** * Created with IntelliJ IDEA. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java index e30df7dd2..8f2155ff2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; /** * [Short one sentence description of this walker] diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java index 4e40f7d49..82e2bd199 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration.covariates; +package org.broadinstitute.gatk.engine.recalibration.covariates; /** * [Short one sentence description of this walker] diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java index 949b61ec1..d8e30983e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java @@ -58,9 +58,9 @@ import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.vcf.VCFHeaderLineCount; import htsjdk.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeAlleleCounts; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java index e1ffbb0f3..6f0bba28e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java @@ -52,9 +52,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; @@ -65,6 +65,7 @@ import htsjdk.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextUtils; +import org.broadinstitute.gatk.utils.variant.ChromosomeCountConstants; import java.util.*; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java index fad666f80..8a0777245 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java index 6fd39555e..f1848260d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java index d71d58853..3cfa0a94a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java index 0972038d6..1d051d5da 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java @@ -52,23 +52,15 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import cern.jet.math.Arithmetic; -import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypesContext; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.QualityUtils; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.gatk.utils.pileup.PileupElement; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java index 54535e32c..6d3dfd6d8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java @@ -51,19 +51,15 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.BaseUtils; -import org.broadinstitute.gatk.utils.help.HelpConstants; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java index 2460e45be..f3a95e6ae 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java @@ -51,15 +51,14 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFHeaderLineType; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java index 9b5778c1d..68da5b951 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java @@ -51,10 +51,10 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; @@ -70,7 +70,6 @@ import org.broadinstitute.gatk.utils.pileup.PileupElement; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import org.broadinstitute.gatk.utils.sam.AlignmentUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java index b511a1b90..07bcd5079 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java @@ -52,13 +52,12 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.tribble.util.popgen.HardyWeinbergCalculation; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.WorkInProgressAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.QualityUtils; import htsjdk.variant.vcf.VCFHeaderLineType; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java index 4c77ffff4..a0148eac2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java index e44ff0635..a89d2ea84 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java @@ -52,9 +52,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java index a30924187..185b5b59c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java @@ -51,16 +51,16 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.samples.Trio; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.gatk.utils.MendelianViolation; +import org.broadinstitute.gatk.engine.samples.MendelianViolation; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java index 49bc74161..57f42ef4b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java index 1f677c6d0..408217af8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java @@ -51,10 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.samples.Sample; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.samples.Trio; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; @@ -62,7 +61,7 @@ import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAn import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.gatk.utils.MendelianViolation; +import org.broadinstitute.gatk.engine.samples.MendelianViolation; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java index 004e5d18f..49db309f3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java @@ -51,10 +51,10 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; @@ -189,7 +189,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati if ( QD < MAX_QD_BEFORE_FIXING ) { return QD; } else { - return IDEAL_HIGH_QD + GenomeAnalysisEngine.getRandomGenerator().nextGaussian() * JITTER_SIGMA; + return IDEAL_HIGH_QD + Utils.getRandomGenerator().nextGaussian() * JITTER_SIGMA; } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java index fbeea3331..038545cf4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java index eb70a19a2..c257a05ff 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java @@ -52,9 +52,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java index b0f298048..e82b485f3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java index 6b7b21b30..f996dd991 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java index 143b16edd..0da2932f5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java index 3791b7912..4db1fbaa7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java @@ -55,12 +55,11 @@ import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.vcf.VCFHeaderLine; -import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.apache.log4j.Logger; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import htsjdk.variant.variantcontext.Genotype; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java index 41f34b5f8..a8714aca2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java @@ -51,12 +51,8 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypesContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java index 4163f7bb7..81d5ee9d0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java index 430c71597..932eced35 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java @@ -51,12 +51,11 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.samples.Sample; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java index 49adb5161..5b4bab87e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java index 45ab38542..ca0dcb8db 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java @@ -56,17 +56,17 @@ import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.recalibration.RecalUtils; -import org.broadinstitute.gatk.utils.recalibration.RecalibrationReport; -import org.broadinstitute.gatk.utils.recalibration.BaseRecalibration; +import org.broadinstitute.gatk.engine.recalibration.RecalUtils; +import org.broadinstitute.gatk.engine.recalibration.RecalibrationReport; +import org.broadinstitute.gatk.engine.recalibration.BaseRecalibration; import java.io.File; import java.io.FileNotFoundException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java index fd87c7f31..3aa4ba5dd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java @@ -55,15 +55,16 @@ import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.CigarElement; import htsjdk.samtools.SAMFileHeader; import htsjdk.tribble.Feature; +import org.broadinstitute.gatk.engine.recalibration.*; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.commandline.Advanced; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.filters.*; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.baq.BAQ; @@ -74,7 +75,7 @@ import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.recalibration.*; -import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.sam.ReadUtils; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java index 53d26c176..c3914216d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java @@ -55,7 +55,7 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.recalibration.EventType; -import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /** diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java index 52a34aa54..aa20c9656 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java @@ -52,9 +52,13 @@ package org.broadinstitute.gatk.tools.walkers.bqsr; import com.google.java.contract.Requires; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.RecalDatum; +import org.broadinstitute.gatk.engine.recalibration.RecalUtils; +import org.broadinstitute.gatk.engine.recalibration.RecalibrationTables; import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; import org.broadinstitute.gatk.utils.recalibration.*; -import org.broadinstitute.gatk.utils.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.PrintStream; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java index e4735505b..d5683504c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java @@ -54,10 +54,10 @@ package org.broadinstitute.gatk.tools.walkers.diagnostics; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.report.GATKReport; import org.broadinstitute.gatk.engine.walkers.LocusWalker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java index 18fe381a3..855d5446c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java @@ -54,9 +54,9 @@ package org.broadinstitute.gatk.tools.walkers.diagnostics; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.ActiveRegionTraversalParameters; import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker; import org.broadinstitute.gatk.engine.walkers.PartitionBy; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java index 9240c56e3..d2cb4439b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java @@ -56,12 +56,11 @@ import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.SampleUtils; import org.broadinstitute.gatk.utils.classloader.PluginManager; import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -70,6 +69,7 @@ import org.broadinstitute.gatk.utils.help.HelpConstants; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.vcf.*; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.io.PrintStream; import java.util.*; @@ -154,7 +154,7 @@ public class DiagnoseTargets extends LocusWalker { intervalListIterator = new PeekableIterator(getToolkit().getIntervals().iterator()); // get all of the unique sample names for the VCF Header - samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); + samples = ReadUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); vcfWriter.writeHeader(new VCFHeader(getHeaderInfo(), samples)); // pre load all the statistics classes because it is costly to operate on the JVM and we only want to do it once. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java index 715ee5b05..4261eee4c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java @@ -51,8 +51,8 @@ package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java index ef83c71e3..d2bca0222 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java @@ -56,11 +56,11 @@ import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Gather; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportGatherer; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportGatherer; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.GenomeLocSortedSet; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java index 4993d5614..54ea7da0a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java @@ -52,6 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; +import org.broadinstitute.gatk.utils.genotyper.AlleleListPermutation; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java index 53523472a..96f432dc1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java @@ -52,11 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.clipping.ReadClipper; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import org.broadinstitute.gatk.utils.collections.Pair; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java index 60799caca..71587fe3e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java @@ -52,7 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import com.google.java.contract.Requires; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.broadinstitute.gatk.utils.MathUtils; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java index 03b3e3374..8d07268d3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java @@ -52,10 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.MathUtils; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java index 0964a74ab..3a65a3a9e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java @@ -51,7 +51,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACset; import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.gatk.utils.haplotype.Haplotype; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java index 693982b2f..c0e2ea95e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java @@ -52,10 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.haplotype.Haplotype; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java index ecb66cdf9..93b7524db 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java @@ -77,10 +77,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index c3208ce8b..b32f291f9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -52,10 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java index 1f73c7140..c73690a84 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java @@ -52,7 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; /** * Encapsulates the data use to make the genotype calls. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java index 60254fdc8..63caf8a14 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java @@ -58,11 +58,12 @@ import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.genotyper.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculator; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationResult; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java index 873318532..f06a40b73 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java @@ -53,6 +53,8 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; import java.util.List; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java index f2413f122..4dfb8d312 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java @@ -52,6 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; /** * Common interface for genotyping models. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java index bc7691e46..dee370eec 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java @@ -51,6 +51,8 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; +import org.broadinstitute.gatk.utils.genotyper.SampleList; + /** * {@link PloidyModel} implementation tailored to work with a homogeneous constant ploidy * across samples and positions. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 10ffeffd2..7ee4a9aca 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -52,10 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.GenomeLoc; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java index 320ccebe7..1589e8374 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java @@ -53,6 +53,9 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.AlleleListPermutation; +import org.broadinstitute.gatk.utils.genotyper.AlleleListUtils; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import java.util.ArrayList; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java index e21494985..1ad1a2241 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java @@ -51,6 +51,8 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; +import org.broadinstitute.gatk.utils.genotyper.SampleList; + /** * Information about the number of chromosome per sample at a given location. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 39a37b642..66be00a08 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -52,10 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java index bf52849d6..b2bd306fc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java @@ -49,12 +49,11 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.engine.arguments; +package org.broadinstitute.gatk.tools.walkers.genotyper; +import org.broadinstitute.gatk.engine.arguments.GenotypeCalculationArgumentCollection; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorImplementation; import org.broadinstitute.gatk.utils.commandline.*; -import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode; -import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode; import org.broadinstitute.gatk.utils.collections.DefaultHashMap; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java index cc3ba9353..08e13da1b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java @@ -52,7 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.broadinstitute.gatk.utils.commandline.*; -import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.tools.walkers.genotyper.StandardCallerArgumentCollection; import org.broadinstitute.gatk.utils.pairhmm.PairHMM; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java index 21f445f7e..2f23f4852 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java @@ -58,25 +58,27 @@ import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; import org.broadinstitute.gatk.engine.filters.BadMateFilter; import org.broadinstitute.gatk.engine.filters.MappingQualityUnavailableFilter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.genotyper.IndexedSampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider; -import org.broadinstitute.gatk.utils.SampleUtils; import org.broadinstitute.gatk.utils.baq.BAQ; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import java.io.PrintStream; @@ -267,7 +269,7 @@ public class UnifiedGenotyper extends LocusWalker, Unif sampleNameSet = Collections.singleton(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME); } else { // get all of the unique sample names - sampleNameSet = SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()); + sampleNameSet = ReadUtils.getSAMFileSamples(toolkit.getSAMFileHeader()); if ( UAC.referenceSampleName != null ) sampleNameSet.remove(UAC.referenceSampleName); } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java index 6b6b66062..1753bb294 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java @@ -56,10 +56,11 @@ import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; import org.apache.log4j.Logger; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationResult; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider; import org.broadinstitute.gatk.utils.BaseUtils; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java index 69175a29c..e97b9ca79 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java @@ -54,8 +54,8 @@ package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import org.apache.log4j.ConsoleAppender; import org.apache.log4j.Logger; import org.apache.log4j.TTCCLayout; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.SimpleTimer; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java index 132a1b7cb..53bfbcbe6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java @@ -56,7 +56,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; import org.broadinstitute.gatk.engine.arguments.GenotypeCalculationArgumentCollection; -import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.tools.walkers.genotyper.StandardCallerArgumentCollection; /** * A single fixed instance AF calculator provider. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java index 31dab29e7..b70765402 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java @@ -52,7 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.SeqGraph; import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java index 3b01d036e..91120f43d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java @@ -53,9 +53,9 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.variant.variantcontext.Allele; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedAlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.MultiSampleEdge; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Path; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Route; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java index f4622fa30..1b9b9e106 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -59,16 +59,18 @@ import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingUtils; +import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingUtils; import org.broadinstitute.gatk.engine.filters.BadMateFilter; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.genotyper.*; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; @@ -88,12 +90,9 @@ import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.gatk.utils.fragments.FragmentCollection; import org.broadinstitute.gatk.utils.fragments.FragmentUtils; -import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils; import org.broadinstitute.gatk.utils.gvcf.GVCFWriter; import org.broadinstitute.gatk.utils.haplotype.Haplotype; -import org.broadinstitute.gatk.utils.haplotype.LDMerger; -import org.broadinstitute.gatk.utils.haplotype.MergeVariantsAcrossHaplotypes; import org.broadinstitute.gatk.utils.haplotypeBAMWriter.HaplotypeBAMWriter; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; @@ -1167,7 +1166,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In } catch ( final Exception e ) { // Capture any exception that might be thrown, and write out the assembly failure BAM if requested if ( captureAssemblyFailureBAM ) { - final SAMFileWriter writer = ReadUtils.createSAMFileWriter("assemblyFailure.bam", getToolkit()); + final SAMFileWriter writer = SAMFileWriterStub.createSAMFileWriter("assemblyFailure.bam", getToolkit()); for ( final GATKSAMRecord read : activeRegion.getReads() ) { writer.addAlignment(read); } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java index c5d0073f2..c68245e7f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java @@ -51,7 +51,7 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.tools.walkers.genotyper.StandardCallerArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Advanced; import org.broadinstitute.gatk.utils.commandline.Argument; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java index 5481cfdeb..2f9dfa288 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java @@ -54,7 +54,10 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.variant.variantcontext.*; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.genotyper.*; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider; import org.broadinstitute.gatk.utils.GenomeLoc; @@ -64,7 +67,6 @@ import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.broadinstitute.gatk.utils.haplotype.EventMap; import org.broadinstitute.gatk.utils.haplotype.Haplotype; -import org.broadinstitute.gatk.utils.haplotype.MergeVariantsAcrossHaplotypes; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java index 57f823dac..cf202bf5f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java @@ -49,16 +49,16 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.haplotype; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.java.contract.Requires; import htsjdk.variant.variantcontext.VariantContext; -import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUtils; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils; -import org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.AlleleListUtils; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import java.util.*; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java index db80ac196..3dae25427 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java @@ -56,9 +56,9 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.Window; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java index 53b4cff58..7d17e7502 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.haplotype; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; @@ -58,6 +58,7 @@ import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import java.util.Arrays; import java.util.Iterator; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java index 403e02988..7e42a8742 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java @@ -49,10 +49,11 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.haplotype; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import java.util.List; import java.util.TreeSet; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java index 3c8b0c40d..1b602604d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java @@ -56,17 +56,17 @@ import com.google.java.contract.Requires; import htsjdk.samtools.SAMUtils; import htsjdk.variant.variantcontext.Allele; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedAlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.broadinstitute.gatk.utils.pairhmm.*; -import org.broadinstitute.gatk.utils.recalibration.covariates.RepeatCovariate; -import org.broadinstitute.gatk.utils.recalibration.covariates.RepeatLengthCovariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.RepeatCovariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.RepeatLengthCovariate; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.io.File; @@ -78,8 +78,6 @@ import java.util.*; public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalculationEngine { private final static Logger logger = Logger.getLogger(PairHMMLikelihoodCalculationEngine.class); - public static final byte BASE_QUALITY_SCORE_THRESHOLD = (byte) 18; // Base quals less than this value are squashed down to min possible qual - private final byte constantGCP; private final double log10globalReadMismappingRate; @@ -189,7 +187,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula private void capMinimumReadQualities(GATKSAMRecord read, byte[] readQuals, byte[] readInsQuals, byte[] readDelQuals) { for( int kkk = 0; kkk < readQuals.length; kkk++ ) { readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG - readQuals[kkk] = ( readQuals[kkk] < BASE_QUALITY_SCORE_THRESHOLD ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] ); + readQuals[kkk] = ( readQuals[kkk] < PairHMM.BASE_QUALITY_SCORE_THRESHOLD ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] ); readInsQuals[kkk] = ( readInsQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readInsQuals[kkk] ); readDelQuals[kkk] = ( readDelQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readDelQuals[kkk] ); } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java index 1f75402b0..7a134a380 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java @@ -52,10 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedAlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; @@ -77,7 +77,7 @@ public class RandomLikelihoodCalculationEngine implements ReadLikelihoodCalculat final AlleleList haplotypes = new IndexedAlleleList<>(assemblyResultSet.getHaplotypeList()); final ReadLikelihoods result = new ReadLikelihoods(samples, haplotypes, reads); final Map alleles = new HashMap<>(haplotypes.alleleCount()); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final int sampleCount = samples.sampleCount(); final int alleleCount = haplotypes.alleleCount(); for (int i = 0; i < sampleCount; i++) { diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java index 14fc080b5..6dbcd161e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java @@ -51,7 +51,7 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java index 0599ee880..5320cb52e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java @@ -55,14 +55,14 @@ import htsjdk.samtools.*; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFSimpleHeaderLine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.tools.walkers.genotyper.*; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; -import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.*; import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; import org.broadinstitute.gatk.utils.pileup.PileupElement; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java index 0652a767c..9806a92e9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java @@ -58,11 +58,10 @@ import htsjdk.samtools.util.StringUtil; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.BAQMode; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.utils.BaseUtils; @@ -80,7 +79,7 @@ import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.sam.AlignmentUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.NWaySAMFileWriter; +import org.broadinstitute.gatk.engine.io.NWaySAMFileWriter; import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.broadinstitute.gatk.utils.text.TextFormattingUtils; import org.broadinstitute.gatk.utils.text.XReadLines; @@ -403,7 +402,7 @@ public class IndelRealigner extends ReadWalker { throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile,ex); } - intervals = intervalsFile.getIntervals(getToolkit()).iterator(); + intervals = intervalsFile.getIntervals(getToolkit().getGenomeLocParser()).iterator(); currentInterval = intervals.hasNext() ? intervals.next() : null; @@ -991,7 +990,7 @@ public class IndelRealigner extends ReadWalker { else { int readsSeen = 0; while ( readsSeen++ < MAX_READS_FOR_CONSENSUSES && altConsensesToPopulate.size() <= MAX_CONSENSUSES) { - int index = GenomeAnalysisEngine.getRandomGenerator().nextInt(altAlignmentsToTest.size()); + int index = Utils.getRandomGenerator().nextInt(altAlignmentsToTest.size()); AlignedRead aRead = altAlignmentsToTest.remove(index); if ( CHECKEARLY ) createAndAddAlternateConsensus1(aRead, altConsensesToPopulate, reference,leftmostIndex); else createAndAddAlternateConsensus(aRead.getReadBases(), altConsensesToPopulate, reference); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java index ba1ad9db2..e6fd8d13b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java @@ -55,9 +55,9 @@ import htsjdk.samtools.Cigar; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java index 27abc48ad..ba9c985db 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java @@ -53,10 +53,10 @@ package org.broadinstitute.gatk.tools.walkers.indels; import com.google.java.contract.Ensures; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedAlleleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedSampleList; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.clipping.ReadClipper; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java index 69ef455d6..7384a70a9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java @@ -57,11 +57,11 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.filters.*; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java index f43d8377c..c01bb9cce 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java @@ -56,15 +56,15 @@ import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.samples.Sample; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.QualityUtils; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java index 0fe20e07d..e8ccaf842 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java @@ -58,17 +58,17 @@ import org.broadinstitute.gatk.utils.commandline.Hidden; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.filters.MappingQualityZeroFilter; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.HasGenomeLocation; -import org.broadinstitute.gatk.utils.SampleUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -82,7 +82,7 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.*; import java.util.*; -import static org.broadinstitute.gatk.utils.variant.GATKVCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.gatk.engine.GATKVCFUtils.getVCFHeadersFromRods; /** * Walks along all variant ROD loci, caching a user-defined window of VariantContext sites, and then finishes phasing them when they go out of range (using upstream and downstream reads). @@ -258,7 +258,7 @@ public class ReadBackedPhasing extends RodWalker vcfSamples = new TreeSet(samplesToPhase == null ? rodNameToHeader.get(trackName).getGenotypeSamples() : samplesToPhase); writer.writeHeader(new VCFHeader(hInfo, vcfSamples)); - Set readSamples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); + Set readSamples = ReadUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); readSamples.retainAll(vcfSamples); if (readSamples.isEmpty()) { String noPhaseString = "No common samples in VCF and BAM headers" + (samplesToPhase == null ? "" : " (limited to sampleToPhase parameters)") + ", so nothing could possibly be phased!"; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java index 4236a1044..2e549263e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java @@ -52,21 +52,21 @@ package org.broadinstitute.gatk.tools.walkers.rnaseq; import htsjdk.samtools.*; +import org.broadinstitute.gatk.engine.io.NWaySAMFileWriter; import org.broadinstitute.gatk.utils.commandline.Advanced; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Hidden; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; import org.broadinstitute.gatk.engine.iterators.RNAReadTransformer; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.engine.walkers.Requires; -import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.clipping.ReadClipper; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; @@ -156,7 +156,7 @@ public class SplitNCigarReads extends ReadWalker { // randomness related variables private static final long RANDOM_SEED = 1252863495; - private static final Random ran = GenomeAnalysisEngine.getRandomGenerator(); + private static final Random ran = Utils.getRandomGenerator(); private Poisson poissonRandom = null; // samples and read groups diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java index ac3dfcdd2..b1c25e44f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java @@ -57,13 +57,13 @@ import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.genotyper.*; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java index 1f5001455..6e4de0860 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java @@ -51,12 +51,12 @@ package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextUtils; +import org.broadinstitute.gatk.utils.Utils; import java.util.ArrayList; import java.util.Collections; @@ -162,13 +162,13 @@ public class KeepAFSpectrumFrequencySelector extends FrequencyModeSelector { // deal with rounding artifacts while (totalSites > numValidationSites) { // take off one from randomly selected bin - int k= GenomeAnalysisEngine.getRandomGenerator().nextInt(NUM_BINS); + int k= Utils.getRandomGenerator().nextInt(NUM_BINS); sitesToChoosePerBin[k]--; totalSites--; } while (totalSites < numValidationSites) { // take off one from randomly selected bin - int k= GenomeAnalysisEngine.getRandomGenerator().nextInt( NUM_BINS); + int k= Utils.getRandomGenerator().nextInt( NUM_BINS); sitesToChoosePerBin[k]++; totalSites++; } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java index 744dd0623..e31188beb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -53,17 +53,17 @@ package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.VariantContextWriter; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java index 2c037bee1..8ade061c8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java @@ -53,16 +53,16 @@ package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.PartitionBy; import org.broadinstitute.gatk.engine.walkers.PartitionType; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.TreeReducible; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java index 08a5865d7..1eb555f2c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java @@ -53,8 +53,8 @@ package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import Jama.Matrix; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import java.util.ArrayList; import java.util.Arrays; @@ -101,7 +101,7 @@ public class GaussianMixtureModel { // initialize random Gaussian means // BUGBUG: this is broken up this way to match the order of calls to rand.nextDouble() in the old code for( final MultivariateGaussian gaussian : gaussians ) { - gaussian.initializeRandomMu( GenomeAnalysisEngine.getRandomGenerator() ); + gaussian.initializeRandomMu( Utils.getRandomGenerator() ); } // initialize means using K-means algorithm @@ -112,7 +112,7 @@ public class GaussianMixtureModel { for( final MultivariateGaussian gaussian : gaussians ) { gaussian.pMixtureLog10 = Math.log10( 1.0 / ((double) gaussians.size()) ); gaussian.sumProb = 1.0 / ((double) gaussians.size()); - gaussian.initializeRandomSigma( GenomeAnalysisEngine.getRandomGenerator() ); + gaussian.initializeRandomSigma( Utils.getRandomGenerator() ); gaussian.hyperParameter_a = priorCounts; gaussian.hyperParameter_b = shrinkage; gaussian.hyperParameter_lambda = dirichletParameter; @@ -152,7 +152,7 @@ public class GaussianMixtureModel { if( numAssigned != 0 ) { gaussian.divideEqualsMu( ((double) numAssigned) ); } else { - gaussian.initializeRandomMu( GenomeAnalysisEngine.getRandomGenerator() ); + gaussian.initializeRandomMu( Utils.getRandomGenerator() ); } } } @@ -279,7 +279,7 @@ public class GaussianMixtureModel { // if it is missing marginalize over the missing dimension by drawing X random values for the missing annotation and averaging the lod if( datum.isNull[iii] ) { for( int ttt = 0; ttt < numIterPerMissingAnnotation; ttt++ ) { - datum.annotations[iii] = GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); // draw a random sample from the standard normal distribution + datum.annotations[iii] = Utils.getRandomGenerator().nextGaussian(); // draw a random sample from the standard normal distribution // evaluate this random data point int gaussianIndex = 0; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java index 023d64f7f..2be4ec01d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java @@ -53,8 +53,8 @@ package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFConstants; @@ -116,7 +116,7 @@ public class VariantDataManager { varianceVector[iii] = theSTD; for( final VariantDatum datum : data ) { // Transform each data point via: (x - mean) / standard deviation - datum.annotations[iii] = ( datum.isNull[iii] ? 0.1 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian() : ( datum.annotations[iii] - theMean ) / theSTD ); + datum.annotations[iii] = ( datum.isNull[iii] ? 0.1 * Utils.getRandomGenerator().nextGaussian() : ( datum.annotations[iii] - theMean ) / theSTD ); } } if( foundZeroVarianceAnnotation ) { @@ -251,7 +251,7 @@ public class VariantDataManager { logger.warn( "WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable." ); } else if( trainingData.size() > VRAC.MAX_NUM_TRAINING_DATA ) { logger.warn( "WARNING: Very large training set detected. Downsampling to " + VRAC.MAX_NUM_TRAINING_DATA + " training variants." ); - Collections.shuffle(trainingData, GenomeAnalysisEngine.getRandomGenerator()); + Collections.shuffle(trainingData, Utils.getRandomGenerator()); return trainingData.subList(0, VRAC.MAX_NUM_TRAINING_DATA); } return trainingData; @@ -299,13 +299,13 @@ public class VariantDataManager { public List getRandomDataForPlotting( final int numToAdd, final List trainingData, final List antiTrainingData, final List evaluationData ) { final List returnData = new ExpandingArrayList<>(); - Collections.shuffle(trainingData, GenomeAnalysisEngine.getRandomGenerator()); - Collections.shuffle(antiTrainingData, GenomeAnalysisEngine.getRandomGenerator()); - Collections.shuffle(evaluationData, GenomeAnalysisEngine.getRandomGenerator()); + Collections.shuffle(trainingData, Utils.getRandomGenerator()); + Collections.shuffle(antiTrainingData, Utils.getRandomGenerator()); + Collections.shuffle(evaluationData, Utils.getRandomGenerator()); returnData.addAll(trainingData.subList(0, Math.min(numToAdd, trainingData.size()))); returnData.addAll(antiTrainingData.subList(0, Math.min(numToAdd, antiTrainingData.size()))); returnData.addAll(evaluationData.subList(0, Math.min(numToAdd, evaluationData.size()))); - Collections.shuffle(returnData, GenomeAnalysisEngine.getRandomGenerator()); + Collections.shuffle(returnData, Utils.getRandomGenerator()); return returnData; } @@ -349,10 +349,10 @@ public class VariantDataManager { try { value = vc.getAttributeAsDouble( annotationKey, Double.NaN ); if( Double.isInfinite(value) ) { value = Double.NaN; } - if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("InbreedingCoeff") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("SOR") && MathUtils.compareDoubles(value, LOG_OF_TWO, 0.01) == 0 ) { value += 0.01 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); } //min SOR is 2.0, then we take ln + if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && annotationKey.equalsIgnoreCase("InbreedingCoeff") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && annotationKey.equalsIgnoreCase("SOR") && MathUtils.compareDoubles(value, LOG_OF_TWO, 0.01) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } //min SOR is 2.0, then we take ln } catch( Exception e ) { value = Double.NaN; // The VQSR works with missing data by marginalizing over the missing dimension when evaluating the Gaussian mixture model } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java index 1cdcb5f5f..e5c7c248b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java @@ -53,10 +53,9 @@ package org.broadinstitute.gatk.tools.walkers.variantrecalibration; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.PartitionBy; import org.broadinstitute.gatk.engine.walkers.PartitionType; import org.broadinstitute.gatk.engine.walkers.RodWalker; @@ -284,7 +283,7 @@ public class VariantRecalibrator extends RodWalker= Math.floor(e)); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java index 7fca0be93..0e95122da 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.Utils; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java index e38ce4687..d16f718be 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java @@ -49,10 +49,10 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.engine.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.recalibration.EventType; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java index bed21cba1..f40ef2602 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java @@ -49,11 +49,12 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; +import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; -import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.utils.recalibration.EventType; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java index 306648ca3..ce374b047 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java @@ -49,10 +49,9 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.engine.recalibration.covariates.*; /** * Created with IntelliJ IDEA. diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java index 877f4e911..66c12a55a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java @@ -49,11 +49,13 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import com.google.java.contract.Requires; -import org.broadinstitute.gatk.tools.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.gatk.utils.recalibration.covariates.*; +import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.RepeatLengthCovariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.RepeatUnitAndLengthCovariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.RepeatUnitCovariate; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java index cc6207ac8..5242414d7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java @@ -51,8 +51,8 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.MannWhitneyU; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -81,9 +81,9 @@ public class RankSumUnitTest { makeDistribution(distribution20_40, 40, skew, observations/2); // shuffle the observations - Collections.shuffle(distribution20, GenomeAnalysisEngine.getRandomGenerator()); - Collections.shuffle(distribution30, GenomeAnalysisEngine.getRandomGenerator()); - Collections.shuffle(distribution20_40, GenomeAnalysisEngine.getRandomGenerator()); + Collections.shuffle(distribution20, Utils.getRandomGenerator()); + Collections.shuffle(distribution30, Utils.getRandomGenerator()); + Collections.shuffle(distribution20_40, Utils.getRandomGenerator()); } private static void makeDistribution(final List result, final int target, final int skew, final int numObservations) { diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java index b1d7de93a..ca10b9a1a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java @@ -51,10 +51,11 @@ package org.broadinstitute.gatk.tools.walkers.bqsr; +import org.broadinstitute.gatk.engine.recalibration.BQSRGatherer; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; -import org.broadinstitute.gatk.utils.recalibration.RecalUtils; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; +import org.broadinstitute.gatk.engine.recalibration.RecalUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java index acb06c4ea..3b4243831 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java @@ -54,7 +54,7 @@ package org.broadinstitute.gatk.tools.walkers.bqsr; import htsjdk.samtools.SAMUtils; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.recalibration.EventType; -import org.broadinstitute.gatk.utils.recalibration.ReadCovariates; +import org.broadinstitute.gatk.engine.recalibration.ReadCovariates; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java index 015460696..585bb2f8d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java @@ -52,8 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.RandomDNA; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList; import org.testng.Assert; import org.testng.SkipException; @@ -69,15 +71,15 @@ import java.util.Set; */ public class AlleleListUnitTester { - private static final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + private static final Random rnd = Utils.getRandomGenerator(); private static final RandomDNA rndDNA = new RandomDNA(rnd); /** * Test that the contents of an allele-list are the ones expected. *

*

- * This method perform various consistency check involving all the {@link org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList} interface methods. - * Therefore calling this method is equivalent to a thorough check of the {@link org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList} aspect of + * This method perform various consistency check involving all the {@link org.broadinstitute.gatk.utils.genotyper.AlleleList} interface methods. + * Therefore calling this method is equivalent to a thorough check of the {@link org.broadinstitute.gatk.utils.genotyper.AlleleList} aspect of * the {@code actual} argument. *

* diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java index ddec1a643..7c3a85d53 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java @@ -52,7 +52,11 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; +import org.broadinstitute.gatk.utils.genotyper.AlleleListPermutation; +import org.broadinstitute.gatk.utils.genotyper.AlleleListUtils; +import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList; import org.testng.Assert; import org.testng.SkipException; import org.testng.annotations.BeforeClass; @@ -62,7 +66,7 @@ import org.testng.annotations.Test; import java.util.*; /** - * Test {@link org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUtils}. + * Test {@link org.broadinstitute.gatk.utils.genotyper.AlleleListUtils}. * * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> */ @@ -121,7 +125,7 @@ public class AlleleListUtilsUnitTest { Assert.assertTrue(AlleleListUtils.equals(selfPermutation,originalAlleleList)); } - private final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + private final Random rnd = Utils.getRandomGenerator(); @Test(dataProvider = "singleAlleleListData", dependsOnMethods = "testEquals") public void testSubsetPermutation(final List alleles1) { diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java index 3dab2af2d..d65770d7b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -53,14 +53,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.*; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; -import org.broadinstitute.gatk.utils.BaseUtils; -import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.pileup.PileupElement; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; @@ -247,10 +243,10 @@ public class ArtificialReadPileupTestProvider { double errorProbability = QualityUtils.qualToErrorProb((byte)phredScaledErrorRate); for (int k=0; k < readBases.length; k++) { - if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < errorProbability) { + if (Utils.getRandomGenerator().nextDouble() < errorProbability) { // random offset int offset = BaseUtils.simpleBaseToBaseIndex(readBases[k]); //0..3 - offset += (GenomeAnalysisEngine.getRandomGenerator().nextInt(3)+1); // adds 1,2 or 3 + offset += (Utils.getRandomGenerator().nextInt(3)+1); // adds 1,2 or 3 offset %= 4; readBases[k] = BaseUtils.baseIndexToSimpleBase(offset); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java index 1dd02c80c..830f3681d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java @@ -53,7 +53,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMUtils; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.MathUtils; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java index a8169dc4f..d3a0864da 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java @@ -53,8 +53,8 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.testng.Assert; import org.testng.annotations.DataProvider; @@ -129,7 +129,7 @@ public class GenotypeLikelihoodCalculatorUnitTest { @Test(dataProvider = "ploidyAndMaximumAlleleAndNewMaximumAlleleData") public void testGenotypeIndexMap(final int ploidy, final int oldAlleleCount, final int newAlleleCount) { - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final int maxAlleleCount = Math.max(oldAlleleCount,newAlleleCount); final int[] alleleMap = new int[newAlleleCount]; final Map> reverseMap = new HashMap<>(oldAlleleCount); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java index 1ec10855f..a96302d0a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java @@ -52,7 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; +import org.broadinstitute.gatk.utils.genotyper.AlleleListUtils; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java index 3e19d2734..e918602da 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java @@ -52,8 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.gatk.tools.walkers.genotyper.PloidyModel; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; /** * General heterogeneous ploidy model. diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java index 89038bdf6..1b5d97994 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java @@ -51,6 +51,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; +import org.broadinstitute.gatk.utils.genotyper.IndexedSampleList; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java index 920e10b09..e19cfca29 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java @@ -53,7 +53,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; import org.broadinstitute.gatk.engine.walkers.Walker; import htsjdk.variant.variantcontext.Allele; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java index 2f8663468..151a2325f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java @@ -53,6 +53,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; +import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -61,7 +62,7 @@ import java.util.*; import static org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUnitTester.assertAlleleList; /** - * Tests {@link org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList}. + * Tests {@link org.broadinstitute.gatk.utils.genotyper.IndexedSampleList}. * * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java index e79512b1e..098c39c66 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java @@ -52,14 +52,15 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.genotyper.IndexedSampleList; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.util.*; /** - * Tests {@link org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList}. + * Tests {@link org.broadinstitute.gatk.utils.genotyper.IndexedSampleList}. * * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> */ @@ -119,7 +120,7 @@ public class IndexedSampleListUnitTest { private static final int[] MAX_SAMPLE_INDEX = { 0, 1, 4, 9, 10000}; - private static final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + private static final Random rnd = Utils.getRandomGenerator(); @DataProvider(name="sampleCountMaxSampleIndexData") diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java index 0e10f741a..70fdf5245 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java @@ -53,8 +53,8 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.genotyper.*; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -93,7 +93,7 @@ public class InfiniteRandomMatingPopulationModelUnitTest { } private AlleleList discardAllelesAtRandom(final AlleleList likelihoods, final int discardAlleleCount) { - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final ArrayList subset = new ArrayList<>(AlleleListUtils.asList(likelihoods)); for (int i = 0; i < discardAlleleCount; i++) { subset.remove(rnd.nextInt(subset.size())); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java index f962260e9..bae62b6c5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.nanoScheduler; +package org.broadinstitute.gatk.tools.walkers.genotyper; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java index 619e96654..f329692ff 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java @@ -49,15 +49,15 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.genotyper; +package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMFileHeader; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.tools.walkers.genotyper.*; +import org.broadinstitute.gatk.utils.genotyper.*; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; @@ -100,7 +100,7 @@ public class ReadLikelihoodsUnitTest } private double[][][] fillWithRandomLikelihoods(final String[] samples, final Allele[] alleles, final ReadLikelihoods result) { - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final double[][][] likelihoods = new double[samples.length][alleles.length][]; for (int s = 0; s < likelihoods.length; s++) { final ReadLikelihoods.Matrix sampleLikelihoods = result.sampleMatrix(s); @@ -545,7 +545,7 @@ public class ReadLikelihoodsUnitTest @DataProvider(name="marginalizationDataSets") public Object[][] marginalizationDataSets() { try { - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final Object[][] result = new Object[SAMPLE_SETS.length * ALLELE_SETS.length * ALLELE_SETS.length][]; int nextIndex = 0; for (int s = 0; s < SAMPLE_SETS.length; s++) { @@ -570,7 +570,7 @@ public class ReadLikelihoodsUnitTest result.put(toAllele,new ArrayList(fromAlleles.length)); final ArrayList remaining = new ArrayList<>(Arrays.asList(fromAlleles)); int nextToIndex = 0; - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); for (int i = 0; i < fromAlleles.length; i++) { final int fromAlleleIndex = rnd.nextInt(remaining.size()); result.get(toAlleles[nextToIndex]).add(remaining.remove(fromAlleleIndex)); @@ -583,7 +583,7 @@ public class ReadLikelihoodsUnitTest @DataProvider(name="dataSets") public Object[][] dataSets() { try { - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final Object[][] result = new Object[SAMPLE_SETS.length * ALLELE_SETS.length][]; int nextIndex = 0; for (int s = 0; s < SAMPLE_SETS.length; s++) @@ -728,7 +728,7 @@ public class ReadLikelihoodsUnitTest } - private final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + private final Random rnd = Utils.getRandomGenerator(); private void testLikelihoodMatrixQueries(final AlleleList alleles, final SampleList samples, final Map> sampleToReads, ReadLikelihoods result) { diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java index 44f8279e1..0aededd99 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java @@ -54,7 +54,9 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.SAMFileHeader; import htsjdk.variant.variantcontext.Allele; +import org.broadinstitute.gatk.utils.genotyper.AlleleList; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.SampleList; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java index f66990d75..c79acccbc 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java @@ -51,8 +51,8 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedSampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; import org.testng.Assert; import java.util.*; @@ -68,8 +68,8 @@ public class SampleListUnitTester { * Test that the contents of a sample-list are the ones expected. * *

- * This method perform various consistency check involving all the {@link org.broadinstitute.gatk.tools.walkers.genotyper.SampleList} interface methods. - * Therefore calling this method is equivalent to a thorough check of the {@link org.broadinstitute.gatk.tools.walkers.genotyper.SampleList} aspect of + * This method perform various consistency check involving all the {@link org.broadinstitute.gatk.utils.genotyper.SampleList} interface methods. + * Therefore calling this method is equivalent to a thorough check of the {@link org.broadinstitute.gatk.utils.genotyper.SampleList} aspect of * the {@code actual} argument. *

* diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java index 565d0cc47..4575e62c1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils; +import org.broadinstitute.gatk.utils.genotyper.IndexedSampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -64,7 +64,7 @@ import java.util.Arrays; import java.util.List; /** - * Test {@link org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUtils}. + * Test {@link org.broadinstitute.gatk.utils.genotyper.AlleleListUtils}. * * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java index 780ab3e0d..4781488a9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java @@ -51,9 +51,9 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.tools.walkers.genotyper.StandardCallerArgumentCollection; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection; +import org.broadinstitute.gatk.utils.Utils; import org.testng.SkipException; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -151,7 +151,7 @@ public class StandardCallerArgumentCollectionUnitTest { public T randomArgumentCollection(final Class clazz) throws IllegalAccessException, InstantiationException { final T result = clazz.newInstance(); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); for (final Field field : clazz.getFields()) { final int fieldModifiers = field.getModifiers(); if (!Modifier.isPublic(fieldModifiers)) diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java index 3f38d20e9..4d7b1568b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java @@ -65,6 +65,8 @@ import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorP import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index e975c11d0..a80bac9a8 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -54,9 +54,9 @@ package org.broadinstitute.gatk.tools.walkers.genotyper; import htsjdk.samtools.util.BlockCompressedInputStream; import htsjdk.tribble.readers.AsciiLineReader; import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; @@ -246,14 +246,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { Arrays.asList(md5)); executeTest("test parallelization (single thread)", spec1); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( myCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1, Arrays.asList(md5)); executeTest("test parallelization (2 threads)", spec2); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( myCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1, diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java index 325fbf962..9fddd1722 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java @@ -54,7 +54,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; import org.broadinstitute.gatk.engine.arguments.GenotypeCalculationArgumentCollection; -import org.broadinstitute.gatk.engine.arguments.StandardCallerArgumentCollection; +import org.broadinstitute.gatk.tools.walkers.genotyper.StandardCallerArgumentCollection; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java index 629bcbbf9..366b90bb7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java @@ -51,12 +51,12 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.tools.walkers.genotyper.AFPriorProvider; import org.broadinstitute.gatk.tools.walkers.genotyper.CustomAFPriorProvider; import org.broadinstitute.gatk.tools.walkers.genotyper.HeterozygosityAFPriorProvider; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -77,7 +77,7 @@ public class AFPriorProviderUnitTest extends BaseTest { @Test(dataProvider="HeterozygosityProviderData") public void testHeterozygosityProvider(final double h, final int useCount, final int minPloidy, final int maxPloidy) { final double het = h / maxPloidy; - final Random rdn = GenomeAnalysisEngine.getRandomGenerator(); + final Random rdn = Utils.getRandomGenerator(); final int[] plodies = new int[useCount]; for (int i = 0; i < useCount; i++) plodies[i] = rdn.nextInt(maxPloidy - minPloidy + 1) + minPloidy; @@ -100,7 +100,7 @@ public class AFPriorProviderUnitTest extends BaseTest { @Test(dataProvider="CustomProviderData") public void testCustomProvider(final int ploidy) { final double[] priors = new double[ploidy]; - final Random rdn = GenomeAnalysisEngine.getRandomGenerator(); + final Random rdn = Utils.getRandomGenerator(); double remaining = 1; final List priorsList = new ArrayList(); for (int i = 0; i < priors.length; i++) { diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java index a41db9386..81afc1816 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java @@ -49,15 +49,12 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.pairhmm; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import org.apache.commons.math.distribution.ExponentialDistribution; -import org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResult; -import org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSet; -import org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.MathUtils; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java index 25aedb149..3f0cb94f3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java @@ -55,7 +55,6 @@ import com.google.caliper.Param; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.haplotype.Haplotype; -import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java index a8a90f37a..b1174e22a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java @@ -60,7 +60,6 @@ import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.RandomDNA; import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; import org.broadinstitute.gatk.utils.haplotype.Haplotype; -import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java index 621ef7b1f..8773bbc63 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java @@ -49,10 +49,11 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.pairhmm; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; -import org.broadinstitute.gatk.tools.walkers.haplotypecaller.ActiveRegionTestDataSetUnitTest; import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.pairhmm.FastLoglessPairHMM; +import org.broadinstitute.gatk.utils.pairhmm.PairHMMReadyHaplotypes; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java index e898829ad..258db39e9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java @@ -53,8 +53,7 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils; -import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; import org.broadinstitute.gatk.utils.pairhmm.FastLoglessPairHMM; import org.broadinstitute.gatk.utils.pairhmm.PairHMM; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java index 528da1762..dfd91ab24 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java @@ -49,10 +49,12 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.haplotype; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.HaplotypeBaseComparator; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 14dd1cf76..9d00c1d0c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -60,7 +60,7 @@ import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.collections.Pair; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java index aae88fbfb..2ef8b7332 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.haplotype; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.broadinstitute.gatk.utils.BaseTest; import org.testng.Assert; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java index ea368e631..b137c3c20 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java @@ -49,10 +49,12 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.haplotype; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.HaplotypeScoreComparator; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java index 1808ac19a..593b3a833 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java @@ -49,10 +49,12 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.haplotype; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotype.HaplotypeSizeAndBaseComparator; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java index 337a91e44..68c6bea73 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.haplotype; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.gatk.utils.BaseTest; @@ -57,6 +57,8 @@ import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.gatk.utils.haplotype.EventMap; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java index cb1f31a84..0040dd7bf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java @@ -61,8 +61,8 @@ import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.pairhmm.PairHMM; -import org.broadinstitute.gatk.utils.recalibration.covariates.RepeatCovariate; -import org.broadinstitute.gatk.utils.recalibration.covariates.RepeatLengthCovariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.RepeatCovariate; +import org.broadinstitute.gatk.engine.recalibration.covariates.RepeatLengthCovariate; import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeSuite; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java index b7d0b037e..4ec4c4cbf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java @@ -49,7 +49,7 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.pairhmm; +package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java index 2c702d0b1..2ce464dd2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java @@ -52,15 +52,12 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; import htsjdk.variant.variantcontext.Allele; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.haplotype.Haplotype; -import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet; -import org.broadinstitute.gatk.utils.pairhmm.FastLoglessPairHMM; -import org.broadinstitute.gatk.utils.pairhmm.FlexibleHMM; -import org.broadinstitute.gatk.utils.pairhmm.PairHMM; +import org.broadinstitute.gatk.utils.pairhmm.*; import org.broadinstitute.gatk.utils.sam.ClippedGATKSAMRecord; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java index 6eb207bf1..f7a4059e0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java @@ -60,6 +60,8 @@ import org.broadinstitute.gatk.tools.walkers.genotyper.*; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java index 13538d304..964d6c151 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java @@ -55,9 +55,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval; // the imports for unit testing. import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier; import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index e47b26758..3d5463d0f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -51,9 +51,8 @@ package org.broadinstitute.gatk.tools.walkers.variantrecalibration; +import org.broadinstitute.gatk.utils.variant.VCIterable; import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; -import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; @@ -340,7 +339,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { final List outputFiles = executeTest("testApplyRecalibrationSnpAndIndelTogether", spec).getFirst(); setPDFsForDeletion(outputFiles); final File VCF = outputFiles.get(0); - for( final VariantContext VC : GATKVCFUtils.readAllVCs(VCF, new VCFCodec()).getSecond() ) { + for( final VariantContext VC : VCIterable.readAllVCs(VCF, new VCFCodec()).getSecond() ) { if( VC != null ) { Assert.assertTrue(VC.isNotFiltered()); // there should only be unfiltered records in the output VCF file } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java index 891ad8d38..8e176089d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java @@ -52,7 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java index a301adc02..d3a145be6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java @@ -52,7 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; import htsjdk.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import htsjdk.variant.vcf.VCFCodec; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java index f72bfc415..b9cfc0949 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java @@ -51,29 +51,22 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; -import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.SAMFileHeader; -import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.collections.Pair; -import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; -import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.io.File; -import java.io.FileNotFoundException; import java.util.*; /** diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java index eaa76becb..08bb0b4a2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java @@ -49,12 +49,13 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.utils.variant; +package org.broadinstitute.gatk.tools.walkers.variantutils; import htsjdk.variant.variantcontext.*; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; @@ -67,7 +68,7 @@ import java.util.Arrays; import java.util.List; /** - * Tests {@link org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger}. + * Tests {@link org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger}. * * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java index 56a07058f..2dafcb70d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java @@ -51,7 +51,7 @@ package org.broadinstitute.gatk.utils.collections; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -68,7 +68,7 @@ public class IndexedSetUnitTest { @Test(dataProvider = "initialCapacityElementCountMaxElementData") public void testCompositionBySingleElementAddition(final int initialCapacity, final int elementCount, final int maxElement) { - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final IndexedSet subject = new IndexedSet<>(initialCapacity); final Set elementSet = new LinkedHashSet<>(); @@ -111,7 +111,7 @@ public class IndexedSetUnitTest { } private List generateElementCollection(final int elementCount, final int maxElement) { - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final List elementList = new ArrayList<>(elementCount); for (int i = 0; i < elementCount; i++) @@ -163,7 +163,7 @@ public class IndexedSetUnitTest { final IndexedSet subject = new IndexedSet<>(elementList); final Set elementSet = new LinkedHashSet<>(elementList); final int removeCount = (subject.size() + 1) / 2; - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); for (int i = 0; i < removeCount; i++) { final int removeIndex = rnd.nextInt(subject.size()); final int removeElement = subject.get(removeIndex); @@ -181,7 +181,7 @@ public class IndexedSetUnitTest { final IndexedSet subject = new IndexedSet<>(elementList); final Set elementSet = new LinkedHashSet<>(elementList); final int removeCount = subject.size(); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); for (int i = 0; i < removeCount; i++) { final int removeIndex = rnd.nextInt(subject.size()); final int removeElement = subject.get(removeIndex); @@ -211,7 +211,7 @@ public class IndexedSetUnitTest { final IndexedSet subject = new IndexedSet<>(elementList); final Set elementSet = new LinkedHashSet<>(elementList); final int removeCount = subject.size(); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); for (int i = 0; i < removeCount; i++) { final int removeIndex = rnd.nextInt(subject.size()); final int removeElement = subject.get(removeIndex); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java index 03f19491f..aeab35ad4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java @@ -51,7 +51,7 @@ package org.broadinstitute.gatk.utils.collections; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -73,7 +73,7 @@ public class IntMaxHeapUnitTest { final IntMaxHeap heap = new IntMaxHeap(initialCapacity); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); for (int i = 0; i < elementCount; i++) { final int v = rnd.nextInt(); @@ -85,7 +85,7 @@ public class IntMaxHeapUnitTest { public void testEmptynessAndSize(final int initialCapacity, final int elementCount) { final IntMaxHeap heap = new IntMaxHeap(initialCapacity); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); Assert.assertEquals(heap.size(),0); Assert.assertTrue(heap.isEmpty()); @@ -101,7 +101,7 @@ public class IntMaxHeapUnitTest { public void testClear(final int initialCapacity, final int elementCount) { final IntMaxHeap heap = new IntMaxHeap(initialCapacity); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); for (int i = 0; i < elementCount; i++) { final int v = rnd.nextInt(); @@ -118,7 +118,7 @@ public class IntMaxHeapUnitTest { final IntMaxHeap addHeap = new IntMaxHeap(initialCapacity); final IntMaxHeap arrayAddHeap = new IntMaxHeap(initialCapacity); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final int[] values = new int[elementCount]; for (int i = 0; i < elementCount; i++) { final int v = rnd.nextInt(); @@ -135,7 +135,7 @@ public class IntMaxHeapUnitTest { public void testRemove(final int initialCapacity, final int elementCount) { final IntMaxHeap heap = new IntMaxHeap(initialCapacity); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); final List values = new ArrayList<>(elementCount); for (int i = 0; i < elementCount; i++) { final int v = rnd.nextInt(); @@ -154,7 +154,7 @@ public class IntMaxHeapUnitTest { public void testPeek(final int initialCapacity, final int elementCount) { final IntMaxHeap heap = new IntMaxHeap(initialCapacity); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); int top = rnd.nextInt(); heap.add(top); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java index 4922e69d6..e00ac7e8e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java @@ -49,16 +49,16 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; // the imports for unit testing. import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffElement; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffEngine; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode; -import org.broadinstitute.gatk.engine.walkers.diffengine.Difference; +import org.broadinstitute.gatk.utils.diffengine.DiffElement; +import org.broadinstitute.gatk.utils.diffengine.DiffEngine; +import org.broadinstitute.gatk.utils.diffengine.DiffNode; +import org.broadinstitute.gatk.utils.diffengine.Difference; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java index 388ba518f..38252223a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java @@ -49,16 +49,16 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; // the imports for unit testing. import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffElement; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffValue; +import org.broadinstitute.gatk.utils.diffengine.DiffElement; +import org.broadinstitute.gatk.utils.diffengine.DiffNode; +import org.broadinstitute.gatk.utils.diffengine.DiffValue; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java index 26b786022..e20ba1625 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java @@ -49,17 +49,17 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; // the imports for unit testing. import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffElement; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffEngine; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffableReader; +import org.broadinstitute.gatk.utils.diffengine.DiffElement; +import org.broadinstitute.gatk.utils.diffengine.DiffEngine; +import org.broadinstitute.gatk.utils.diffengine.DiffNode; +import org.broadinstitute.gatk.utils.diffengine.DiffableReader; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java index 685514f34..cee923476 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java @@ -49,16 +49,16 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; // the imports for unit testing. import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffElement; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffNode; -import org.broadinstitute.gatk.engine.walkers.diffengine.Difference; +import org.broadinstitute.gatk.utils.diffengine.DiffElement; +import org.broadinstitute.gatk.utils.diffengine.DiffNode; +import org.broadinstitute.gatk.utils.diffengine.Difference; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java index 5643e3030..1c34405b0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java @@ -55,7 +55,6 @@ package org.broadinstitute.gatk.utils.pairhmm; // the imports for unit testing. import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.QualityUtils; @@ -252,8 +251,8 @@ public class PairHMMUnitTest extends BaseTest { @DataProvider(name = "OptimizedLikelihoodTestProvider") public Object[][] makeOptimizedLikelihoodTests() { - GenomeAnalysisEngine.resetRandomGenerator(); - final Random random = GenomeAnalysisEngine.getRandomGenerator(); + Utils.resetRandomGenerator(); + final Random random = Utils.getRandomGenerator(); final List baseQuals = EXTENSIVE_TESTING ? Arrays.asList(10, 30, 40, 60) : Arrays.asList(30); final List indelQuals = EXTENSIVE_TESTING ? Arrays.asList(20, 40, 60) : Arrays.asList(40); final List gcps = EXTENSIVE_TESTING ? Arrays.asList(10, 20, 30) : Arrays.asList(10); diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml index 5cde74b85..94406680d 100644 --- a/public/external-example/pom.xml +++ b/public/external-example/pom.xml @@ -49,7 +49,15 @@ org.broadinstitute.gatk - gatk-tools-public + gatk-utils + ${gatk.version} + test-jar + test + + + + org.broadinstitute.gatk + gatk-engine ${gatk.version} test-jar test @@ -82,7 +90,7 @@ org.broadinstitute.gatk - gatk-engine + gatk-utils ${gatk.version} example-resources tar.bz2 @@ -112,8 +120,7 @@ ${project.build.outputDirectory} org.broadinstitute.gatk - - gatk-tools-public + gatk-utils ${gatk.version} 2g diff --git a/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java b/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java index 1834c4a4a..8dedbdd59 100644 --- a/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java +++ b/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java @@ -26,9 +26,9 @@ package org.mycompany.app; import org.broadinstitute.gatk.utils.commandline.Output; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.LocusWalker; import java.io.PrintStream; diff --git a/public/gatk-engine/pom.xml b/public/gatk-engine/pom.xml index 593c1feb4..6d2696c7a 100644 --- a/public/gatk-engine/pom.xml +++ b/public/gatk-engine/pom.xml @@ -24,6 +24,22 @@ gatk-utils ${project.version} + + net.java.dev.jets3t + jets3t + + + org.simpleframework + simple-xml + + + + ${project.groupId} + gatk-utils + ${project.version} + test-jar + test + com.google.caliper @@ -34,16 +50,6 @@ - - org.apache.maven.plugins - maven-assembly-plugin - - - example-resources - ${gatk.generate-resources.phase} - - - org.apache.maven.plugins maven-resources-plugin @@ -54,8 +60,6 @@ - org.apache.maven.plugins maven-invoker-plugin diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java index b8221bb16..a2bb4afd9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java @@ -29,16 +29,16 @@ import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor; import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.io.stubs.OutputStreamArgumentTypeDescriptor; import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterArgumentTypeDescriptor; import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; import org.broadinstitute.gatk.engine.walkers.Walker; -import org.broadinstitute.gatk.utils.crypt.CryptUtils; -import org.broadinstitute.gatk.utils.crypt.GATKKey; +import org.broadinstitute.gatk.engine.crypt.CryptUtils; +import org.broadinstitute.gatk.engine.crypt.GATKKey; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.text.ListFileUtils; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java index f88c413bb..afecc2e12 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java @@ -25,14 +25,13 @@ package org.broadinstitute.gatk.engine; -import picard.PicardException; import htsjdk.samtools.SAMException; import htsjdk.tribble.TribbleException; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; -import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager; +import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager; import org.broadinstitute.gatk.engine.walkers.Attribution; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -112,9 +111,6 @@ public class CommandLineGATK extends CommandLineExecutable { // We can generate Tribble Exceptions in weird places when e.g. VCF genotype fields are // lazy loaded, so they aren't caught elsewhere and made into User Exceptions exitSystemWithUserError(e); - } catch(PicardException e) { - // TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedGATKExceptions? - exitSystemWithError(e); } catch (SAMException e) { checkForMaskedUserErrors(e); exitSystemWithSamError(e); @@ -178,16 +174,6 @@ public class CommandLineGATK extends CommandLineExecutable { return header; } - public static String getVersionNumber() { - ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); - return headerInfo.containsKey("org.broadinstitute.gatk.tools.version") ? headerInfo.getString("org.broadinstitute.gatk.tools.version") : ""; - } - - public static String getBuildTime() { - ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); - return headerInfo.containsKey("build.timestamp") ? headerInfo.getString("build.timestamp") : ""; - } - /** * If the user supplied any additional attribution, return it here. * @return Additional attribution if supplied by the user. Empty (non-null) list otherwise. diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java index 6baa7b654..883ed7fd8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.variant; +package org.broadinstitute.gatk.engine; import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; @@ -39,14 +39,13 @@ import htsjdk.tribble.index.tabix.TabixFormat; import htsjdk.tribble.index.tabix.TabixIndexCreator; import htsjdk.tribble.readers.LineIterator; import htsjdk.tribble.readers.PositionalBufferedStream; +import org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor; import org.broadinstitute.gatk.utils.commandline.RodBinding; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.gatk.utils.collections.Pair; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.*; +import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; import java.io.File; import java.io.FileInputStream; @@ -210,7 +209,7 @@ public class GATKVCFUtils { * @return */ public static IndexCreator getIndexCreator(GATKVCFIndexType type, int parameter, File outFile, SAMSequenceDictionary sequenceDictionary) { - if (VCFWriterArgumentTypeDescriptor.isCompressed(outFile.toString())) { + if (ArgumentTypeDescriptor.isCompressed(outFile.toString())) { if (type != GATKVCFUtils.DEFAULT_INDEX_TYPE || parameter != GATKVCFUtils.DEFAULT_INDEX_PARAMETER) logger.warn("Creating Tabix index for " + outFile + ", ignoring user-specified index type and parameter"); @@ -232,58 +231,6 @@ public class GATKVCFUtils { return idxCreator; } - /** - * Utility class to read all of the VC records from a file - * - * @param file - * @param codec - * @return - * @throws IOException - */ - public final static Pair> readAllVCs( final File file, final FeatureCodec codec) throws IOException { - // read in the features - SOURCE source = codec.makeSourceFromStream(new FileInputStream(file)); - FeatureCodecHeader header = codec.readHeader(source); - final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue(); - return new Pair<>(vcfHeader, new VCIterable<>(source, codec, vcfHeader)); - } - - public static class VCIterable implements Iterable, Iterator { - final SOURCE source; - final FeatureCodec codec; - final VCFHeader header; - - private VCIterable(final SOURCE source, final FeatureCodec codec, final VCFHeader header) { - this.source = source; - this.codec = codec; - this.header = header; - } - - @Override - public Iterator iterator() { - return this; - } - - @Override - public boolean hasNext() { - return ! codec.isDone(source); - } - - @Override - public VariantContext next() { - try { - final VariantContext vc = codec.decode(source); - return vc == null ? null : vc.fullyDecode(header, false); - } catch ( IOException e ) { - throw new RuntimeException(e); - } - } - - @Override - public void remove() { - } - } - /** * Read all of the VCF records from source into memory, returning the header and the VariantContexts * diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java index abb699301..6e2343d5d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java @@ -34,31 +34,30 @@ import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.variant.vcf.VCFConstants; import org.apache.log4j.Logger; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.engine.datasources.reads.*; import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.engine.executive.MicroScheduler; import org.broadinstitute.gatk.engine.filters.FilterManager; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.filters.ReadGroupBlackListFilter; import org.broadinstitute.gatk.engine.io.OutputTracker; -import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub; import org.broadinstitute.gatk.engine.io.stubs.Stub; -import org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.engine.iterators.ReadTransformersMode; import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; -import org.broadinstitute.gatk.engine.refdata.tracks.IndexDictionaryUtils; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.refdata.tracks.IndexDictionaryUtils; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.engine.samples.SampleDB; import org.broadinstitute.gatk.engine.samples.SampleDBBuilder; import org.broadinstitute.gatk.engine.walkers.*; -import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList; -import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.IndexedSampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleList; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.classloader.PluginManager; import org.broadinstitute.gatk.utils.commandline.*; @@ -66,8 +65,9 @@ import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.interval.IntervalUtils; import org.broadinstitute.gatk.utils.progressmeter.ProgressMeter; -import org.broadinstitute.gatk.utils.recalibration.BQSRArgumentSet; +import org.broadinstitute.gatk.engine.recalibration.BQSRArgumentSet; import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.broadinstitute.gatk.utils.text.XReadLines; import org.broadinstitute.gatk.utils.threading.ThreadEfficiencyMonitor; @@ -165,7 +165,7 @@ public class GenomeAnalysisEngine { /** * A currently hacky unique name for this GATK instance */ - private String myName = "GATK_" + Math.abs(getRandomGenerator().nextInt()); + private String myName = "GATK_" + Math.abs(Utils.getRandomGenerator().nextInt()); /** * our walker manager @@ -230,15 +230,6 @@ public class GenomeAnalysisEngine { */ private long runtimeLimitInNanoseconds = -1; - /** - * Static random number generator and seed. - */ - private static final long GATK_RANDOM_SEED = 47382911L; - private static Random randomGenerator = new Random(GATK_RANDOM_SEED); - public static Random getRandomGenerator() { return randomGenerator; } - public static void resetRandomGenerator() { randomGenerator.setSeed(GATK_RANDOM_SEED); } - public static void resetRandomGenerator(long seed) { randomGenerator.setSeed(seed); } - /** * Base Quality Score Recalibration helper object */ @@ -274,7 +265,7 @@ public class GenomeAnalysisEngine { throw new ReviewedGATKException("The walker passed to GenomeAnalysisEngine can not be null."); if (args.nonDeterministicRandomSeed) - resetRandomGenerator(System.currentTimeMillis()); + Utils.resetRandomGenerator(System.currentTimeMillis()); // if the use specified an input BQSR recalibration table then enable on the fly recalibration if (args.BQSR_RECAL_FILE != null) @@ -490,10 +481,31 @@ public class GenomeAnalysisEngine { DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker); DownsamplingMethod method = commandLineMethod != null ? commandLineMethod : walkerMethod; - method.checkCompatibilityWithWalker(walker); + checkCompatibilityWithWalker(method, walker); return method; } + private static void checkCompatibilityWithWalker( DownsamplingMethod method, Walker walker ) { + // Refactored from DownsamplingMethod + final DownsampleType type = method.type; + final Integer toCoverage = method.toCoverage; + final boolean isLocusTraversal = walker instanceof LocusWalker || walker instanceof ActiveRegionWalker; + + if ( isLocusTraversal && type == DownsampleType.ALL_READS && toCoverage != null ) { + throw new UserException("Downsampling to coverage with the ALL_READS method for locus-based traversals (eg., LocusWalkers) is not currently supported (though it is supported for ReadWalkers)."); + } + + // For locus traversals, ensure that the dcov value (if present) is not problematically low + if ( isLocusTraversal && type != DownsampleType.NONE && toCoverage != null && + toCoverage < DownsamplingMethod.MINIMUM_SAFE_COVERAGE_TARGET_FOR_LOCUS_BASED_TRAVERSALS ) { + throw new UserException(String.format("Locus-based traversals (ie., Locus and ActiveRegion walkers) require " + + "a minimum -dcov value of %d when downsampling to coverage. Values less " + + "than this can produce problematic downsampling artifacts while providing " + + "only insignificant improvements in memory usage in most cases.", + DownsamplingMethod.MINIMUM_SAFE_COVERAGE_TARGET_FOR_LOCUS_BASED_TRAVERSALS)); + } + } + protected void setDownsamplingMethod(DownsamplingMethod method) { argCollection.setDownsamplingMethod(method); } @@ -726,7 +738,7 @@ public class GenomeAnalysisEngine { * Setup the intervals to be processed */ protected void initializeIntervals() { - intervals = IntervalUtils.parseIntervalArguments(this.referenceDataSource, argCollection.intervalArguments); + intervals = IntervalUtils.parseIntervalArguments(this.referenceDataSource.getReference(), argCollection.intervalArguments); } /** @@ -1012,12 +1024,7 @@ public class GenomeAnalysisEngine { } public boolean lenientVCFProcessing() { - return lenientVCFProcessing(argCollection.unsafe); - } - - public static boolean lenientVCFProcessing(final ValidationExclusion.TYPE val) { - return val == ValidationExclusion.TYPE.ALL - || val == ValidationExclusion.TYPE.LENIENT_VCF_PROCESSING; + return ValidationExclusion.lenientVCFProcessing(argCollection.unsafe); } /** @@ -1275,6 +1282,6 @@ public class GenomeAnalysisEngine { * @return never {@code null}. */ public SampleList getReadSampleList() { - return new IndexedSampleList(SampleUtils.getSAMFileSamples(getSAMFileHeader())); + return new IndexedSampleList(ReadUtils.getSAMFileSamples(getSAMFileHeader())); } } diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java index 6ee9ad3a4..0f6aee60c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java @@ -26,11 +26,10 @@ package org.broadinstitute.gatk.engine; import htsjdk.samtools.SAMFileHeader; -import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.ValidationStringency; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.utils.ValidationExclusion; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java index 77fc17083..eb98e0bb4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java @@ -23,13 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils; +package org.broadinstitute.gatk.engine; -import htsjdk.samtools.SAMFileHeader; -import htsjdk.samtools.SAMReadGroupRecord; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import org.broadinstitute.gatk.utils.collections.Pair; import htsjdk.variant.vcf.VCFHeader; @@ -53,34 +49,6 @@ public class SampleUtils { */ private SampleUtils() {} - /** - * Pull out the samples from a SAMFileHeader; - * note that we use a TreeSet so that they are sorted - * - * @param header the sam file header - * @return list of strings representing the sample names - */ - public static Set getSAMFileSamples(final SAMFileHeader header) { - // get all of the unique sample names - final Set samples = new TreeSet(); - List readGroups = header.getReadGroups(); - for ( SAMReadGroupRecord readGroup : readGroups ) - samples.add(readGroup.getSample()); - return samples; - } - - - /** - * Same as @link getSAMFileSamples but gets all of the samples - * in the SAM files loaded by the engine - * - * @param engine engine - * @return samples - */ - public static Set getSAMFileSamples(GenomeAnalysisEngine engine) { - return SampleUtils.getSAMFileSamples(engine.getSAMFileHeader()); - } - /** * Gets all of the unique sample names from all VCF rods input by the user * diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java index fb9d48903..9ea5a3c31 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java @@ -28,13 +28,14 @@ package org.broadinstitute.gatk.engine; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.commandline.Hidden; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.engine.filters.FilterManager; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.utils.classloader.PluginManager; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.ResourceBundleExtractorDoclet; import org.broadinstitute.gatk.utils.text.TextFormattingUtils; @@ -153,6 +154,16 @@ public class WalkerManager extends PluginManager { return getPluginsByName().get(walkerName); } + /** + * Rather than use the default exception, return a MalformedWalkerArgumentsException. + * @param errorMessage error message from formatErrorMessage() + * @return - A MalformedWalkerArgumentsException with errorMessage + */ + @Override + protected UserException createMalformedArgumentException(final String errorMessage) { + return new UserException.MalformedWalkerArgumentsException(errorMessage); + } + /** * Gets the data source for the provided walker. * @param walkerClass The class of the walker. diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java index 05834f71b..575c195b4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java @@ -26,16 +26,17 @@ package org.broadinstitute.gatk.engine.arguments; import htsjdk.samtools.ValidationStringency; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; import org.broadinstitute.gatk.engine.samples.PedigreeValidationType; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.baq.BAQ; import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import java.io.File; import java.util.ArrayList; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java index d6ccd3231..cbbbe47e1 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.crypt; +package org.broadinstitute.gatk.engine.crypt; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.io.IOUtils; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java index ab21a2a17..42a88b9d0 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.crypt; +package org.broadinstitute.gatk.engine.crypt; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java index 56ecce2ef..4bcecbcad 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java @@ -25,7 +25,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.engine.iterators.GenomeLocusIterator; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java index 900612a49..777e23cb8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java @@ -25,7 +25,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; /** * User: hanna * Date: May 12, 2009 diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java index 9100905f3..1525c381a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.engine.datasources.providers; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.gatk.engine.refdata.RODRecordListImpl; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.RODRecordListImpl; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import java.util.Collection; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java index 23f4f73e8..4dfc31d86 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java @@ -26,12 +26,10 @@ package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.util.PeekableIterator; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.datasources.reads.ReadShard; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java index b53505097..d4278c9b2 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java @@ -26,7 +26,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.reference.ReferenceSequence; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.engine.walkers.Window; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java index 9bc37e549..11437cf2c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java @@ -25,9 +25,8 @@ package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.locusiterator.LocusIterator; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java index 2dd42c1cc..17e8c4290 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java @@ -25,11 +25,10 @@ package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import java.util.ArrayList; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java index f244e504d..197abd49a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java @@ -25,7 +25,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; import org.broadinstitute.gatk.utils.collections.Pair; import java.util.*; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java index 1d73501bd..dea8acf5f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java @@ -27,19 +27,10 @@ package org.broadinstitute.gatk.engine.datasources.providers; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.engine.datasources.reads.ReadShard; -import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; - -import java.util.ArrayList; -import java.util.Collection; -import java.util.List; /** a ROD view for reads. This provides the Read traversals a way of getting a RefMetaDataTracker */ public class ReadBasedReferenceOrderedView extends IntervalReferenceOrderedView { diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java index 14d5827a3..c7b2575be 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java @@ -26,7 +26,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.GenomeLoc; /* * Copyright (c) 2009 The Broad Institute diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java index 8acfad0b1..f9629f5c8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java @@ -28,7 +28,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.gatk.engine.datasources.reads.Shard; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.GenomeLocParser; import java.util.Collection; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java index 160dbd585..ec879fdfd 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java @@ -26,7 +26,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import java.util.Arrays; import java.util.Collection; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java index 9f3db5143..3be983d4a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java @@ -25,7 +25,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; public interface ReferenceOrderedView extends View { diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java index 21cb3efa6..297ccbedd 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java @@ -25,12 +25,11 @@ package org.broadinstitute.gatk.engine.datasources.providers; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.collections.RODMergingIterator; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java index 1e30d6c38..178d440bf 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java @@ -29,7 +29,7 @@ import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.GATKBAMFileSpan; import htsjdk.samtools.GATKChunk; import htsjdk.samtools.util.BlockCompressedFilePointerUtil; -import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.util.LinkedList; import java.util.List; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java index a80b0a475..aca33e411 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java @@ -34,6 +34,7 @@ import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.GATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.io.File; import java.io.IOException; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java index 1ea8d39aa..f916bc185 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java @@ -36,6 +36,7 @@ import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.util.*; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java index 11fecb661..125d4f731 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java @@ -29,6 +29,7 @@ import htsjdk.samtools.GATKBAMFileSpan; import htsjdk.samtools.GATKChunk; import htsjdk.samtools.util.BlockCompressedInputStream; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.io.IOException; import java.io.InputStream; @@ -100,7 +101,7 @@ public class BlockInputStream extends InputStream { */ BlockInputStream(final BGZFBlockLoadingDispatcher dispatcher, final SAMReaderID reader, final boolean validate) { this.reader = reader; - this.length = reader.samFile.length(); + this.length = reader.getSamFile().length(); buffer = ByteBuffer.wrap(new byte[64*1024]); buffer.order(ByteOrder.LITTLE_ENDIAN); @@ -122,7 +123,7 @@ public class BlockInputStream extends InputStream { try { if(validate) { System.out.printf("BlockInputStream %s: BGZF block validation mode activated%n",this); - validatingInputStream = new BlockCompressedInputStream(reader.samFile); + validatingInputStream = new BlockCompressedInputStream(reader.getSamFile()); // A bug in ValidatingInputStream means that calling getFilePointer() immediately after initialization will result in an NPE. // Poke the stream to start reading data. validatingInputStream.available(); diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java index 8d5ab3b03..7f6653888 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java @@ -27,16 +27,13 @@ package org.broadinstitute.gatk.engine.datasources.reads; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.io.FileInputStream; import java.io.IOException; -import java.util.Collection; import java.util.HashMap; import java.util.LinkedHashMap; -import java.util.LinkedList; -import java.util.List; import java.util.Map; -import java.util.Queue; /** * Caches frequently used file handles. Right now, caches only a single file handle. diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java index 99d9def5a..4ea4aabf9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java @@ -36,6 +36,7 @@ import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; import org.broadinstitute.gatk.utils.interval.IntervalUtils; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.util.*; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java index 28d4faf2c..4714df9b7 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java @@ -29,6 +29,7 @@ import htsjdk.samtools.SAMFileSpan; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.util.List; import java.util.Map; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java index d4321da3b..d8ae3bf55 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java @@ -27,12 +27,12 @@ package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.util.PeekableIterator; import htsjdk.samtools.*; -import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIteratorAdapter; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIteratorAdapter; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.util.*; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java index 0fc06fcce..4c4759b26 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java @@ -33,8 +33,7 @@ import htsjdk.samtools.util.RuntimeIOException; import org.apache.log4j.Logger; import org.broadinstitute.gatk.engine.ReadMetrics; import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; -import org.broadinstitute.gatk.engine.downsampling.*; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.engine.filters.CountingFilteringIterator; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.iterators.*; @@ -42,16 +41,18 @@ import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.GenomeLocSortedSet; import org.broadinstitute.gatk.utils.SimpleTimer; -import org.broadinstitute.gatk.utils.baq.ReadTransformingIterator; +import org.broadinstitute.gatk.engine.iterators.ReadTransformingIterator; +import org.broadinstitute.gatk.utils.downsampling.*; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIteratorAdapter; import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.io.File; -import java.lang.reflect.InvocationTargetException; -import java.lang.reflect.Method; import java.util.*; import java.util.concurrent.Callable; @@ -297,8 +298,8 @@ public class SAMDataSource { // Determine the sort order. for(SAMReaderID readerID: readerIDs) { - if (! readerID.samFile.canRead() ) - throw new UserException.CouldNotReadInputFile(readerID.samFile,"file is not present or user does not have appropriate permissions. " + + if (! readerID.getSamFile().canRead() ) + throw new UserException.CouldNotReadInputFile(readerID.getSamFile(),"file is not present or user does not have appropriate permissions. " + "Please check that the file is present and readable and try again."); // Get the sort order, forcing it to coordinate if unsorted. @@ -308,7 +309,7 @@ public class SAMDataSource { headers.put(readerID,header); if ( header.getReadGroups().isEmpty() ) { - throw new UserException.MalformedBAM(readers.getReaderID(reader).samFile, + throw new UserException.MalformedBAM(readers.getReaderID(reader).getSamFile(), "SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups"); } @@ -361,7 +362,7 @@ public class SAMDataSource { } for(SAMReaderID id: readerIDs) { - File indexFile = findIndexFile(id.samFile); + File indexFile = findIndexFile(id.getSamFile()); if(indexFile != null) bamIndices.put(id,new GATKBAMIndex(indexFile)); } @@ -410,7 +411,7 @@ public class SAMDataSource { * @return the file actually associated with the id. */ public File getSAMFile(SAMReaderID id) { - return id.samFile; + return id.getSamFile(); } /** @@ -585,10 +586,10 @@ public class SAMDataSource { iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id)); } } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes - throw new UserException.MalformedBAM(id.samFile, e.getMessage()); + throw new UserException.MalformedBAM(id.getSamFile(), e.getMessage()); } - iterator = new MalformedBAMErrorReformatingIterator(id.samFile, iterator); + iterator = new MalformedBAMErrorReformatingIterator(id.getSamFile(), iterator); if(shard.getGenomeLocs().size() > 0) iterator = new IntervalOverlapFilteringIterator(iterator,shard.getGenomeLocs()); @@ -603,7 +604,7 @@ public class SAMDataSource { return applyDecoratingIterators(readMetrics, enableVerification, readProperties.useOriginalBaseQualities(), - new ReleasingIterator(readers,GATKSAMIteratorAdapter.adapt(mergingIterator)), + new ReleasingIterator(readers, GATKSAMIteratorAdapter.adapt(mergingIterator)), readProperties.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION), readProperties.getSupplementalFilters(), readProperties.getReadTransformers(), @@ -867,7 +868,7 @@ public class SAMDataSource { inputStreams.put(init.readerID, init.blockInputStream); // get from initializer } - logger.debug(String.format("Processing file (%d of %d) %s...", readerNumber++, totalNumberOfFiles, readerID.samFile)); + logger.debug(String.format("Processing file (%d of %d) %s...", readerNumber++, totalNumberOfFiles, readerID.getSamFile())); readers.put(init.readerID,init.reader); if ( ++nExecutedTotal % tickSize == 0) { double tickInSec = (timer.currentTime() - lastTick) / 1000.0; @@ -1064,21 +1065,21 @@ public class SAMDataSource { } public ReaderInitializer call() { - final File indexFile = findIndexFile(readerID.samFile); + final File indexFile = findIndexFile(readerID.getSamFile()); try { if (threadAllocation.getNumIOThreads() > 0) blockInputStream = new BlockInputStream(dispatcher,readerID,false); - reader = new SAMFileReader(readerID.samFile,indexFile,false); + reader = new SAMFileReader(readerID.getSamFile(),indexFile,false); } catch ( RuntimeIOException e ) { - throw new UserException.CouldNotReadInputFile(readerID.samFile, e); + throw new UserException.CouldNotReadInputFile(readerID.getSamFile(), e); } catch ( SAMFormatException e ) { - throw new UserException.MalformedBAM(readerID.samFile, e.getMessage()); + throw new UserException.MalformedBAM(readerID.getSamFile(), e.getMessage()); } // Picard is throwing a RuntimeException here when BAMs are malformed with bad headers (and so look like SAM files). // Let's keep this separate from the SAMFormatException (which ultimately derives from RuntimeException) case, // just in case we want to change this behavior later. catch ( RuntimeException e ) { - throw new UserException.MalformedBAM(readerID.samFile, e.getMessage()); + throw new UserException.MalformedBAM(readerID.getSamFile(), e.getMessage()); } reader.setSAMRecordFactory(factory); reader.enableFileSource(true); diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java index cc8944ce3..eb9ec480a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java @@ -30,10 +30,11 @@ import htsjdk.samtools.SAMFileSpan; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.engine.ReadMetrics; import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.util.Collections; import java.util.List; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java index 9105b4cf8..231bbc4ef 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java @@ -33,7 +33,7 @@ import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.datasources.reads.FilePointer; import org.broadinstitute.gatk.engine.datasources.reads.IntervalSharder; import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java index 6fdbea3a0..6b7bf2187 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java @@ -56,40 +56,7 @@ public class ReferenceDataSource { * @param fastaFile Fasta file to be used as reference */ public ReferenceDataSource(File fastaFile) { - // does the fasta file exist? check that first... - if (!fastaFile.exists()) - throw new UserException("The fasta file you specified (" + fastaFile.getAbsolutePath() + ") does not exist."); - - final boolean isGzipped = fastaFile.getAbsolutePath().endsWith(".gz"); - if ( isGzipped ) { - throw new UserException.CannotHandleGzippedRef(); - } - - final File indexFile = new File(fastaFile.getAbsolutePath() + ".fai"); - - // determine the name for the dict file - final String fastaExt = fastaFile.getAbsolutePath().endsWith("fa") ? "\\.fa$" : "\\.fasta$"; - final File dictFile = new File(fastaFile.getAbsolutePath().replaceAll(fastaExt, ".dict")); - - // It's an error if either the fai or dict file does not exist. The user is now responsible - // for creating these files. - if (!indexFile.exists()) { - throw new UserException.MissingReferenceFaiFile(indexFile, fastaFile); - } - if (!dictFile.exists()) { - throw new UserException.MissingReferenceDictFile(dictFile, fastaFile); - } - - // Read reference data by creating an IndexedFastaSequenceFile. - try { - reference = new CachingIndexedFastaSequenceFile(fastaFile); - } - catch (IllegalArgumentException e) { - throw new UserException.CouldNotReadInputFile(fastaFile, "Could not read reference sequence. The FASTA must have either a .fasta or .fa extension", e); - } - catch (Exception e) { - throw new UserException.CouldNotReadInputFile(fastaFile, e); - } + reference = CachingIndexedFastaSequenceFile.checkAndCreate(fastaFile); } /** diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java index 762eb0b44..6920ba242 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java @@ -26,12 +26,12 @@ package org.broadinstitute.gatk.engine.datasources.rmd; import htsjdk.samtools.SAMSequenceDictionary; -import org.broadinstitute.gatk.engine.refdata.SeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.gatk.engine.refdata.utils.FlashBackIterator; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.refdata.SeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.utils.refdata.utils.FlashBackIterator; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java index 9d9e7c87f..c88b9b7f2 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java @@ -27,11 +27,11 @@ package org.broadinstitute.gatk.engine.datasources.rmd; import htsjdk.samtools.SAMSequenceDictionary; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.refdata.SeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.refdata.SeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java index 293bb1ce5..fc68b9c7a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java @@ -38,7 +38,7 @@ import org.broadinstitute.gatk.engine.io.OutputTracker; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.engine.traversals.TraversalEngine; import org.broadinstitute.gatk.engine.walkers.Walker; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.broadinstitute.gatk.utils.threading.ThreadEfficiencyMonitor; import java.util.Collection; @@ -93,7 +93,7 @@ public class LinearMicroScheduler extends MicroScheduler { if(shard.getShardType() == Shard.ShardType.LOCUS) { WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), - getReadIterator(shard), shard.getGenomeLocs(), SampleUtils.getSAMFileSamples(engine)); + getReadIterator(shard), shard.getGenomeLocs(), ReadUtils.getSAMFileSamples(engine.getSAMFileHeader())); for(WindowMaker.WindowMakerIterator iterator: windowMaker) { ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),engine.getGenomeLocParser(),iterator.getLocus(),iterator,reference,rods); Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit()); diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java index e192b9a72..f9660a94a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java @@ -35,7 +35,7 @@ import org.broadinstitute.gatk.engine.datasources.reads.Shard; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.gatk.engine.io.OutputTracker; import org.broadinstitute.gatk.engine.iterators.NullSAMIterator; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.engine.traversals.*; import org.broadinstitute.gatk.engine.walkers.*; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java index c8483298b..496178d88 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java @@ -27,16 +27,15 @@ package org.broadinstitute.gatk.engine.executive; import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.engine.datasources.reads.Shard; -import org.broadinstitute.gatk.engine.iterators.GATKSAMRecordIterator; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecordIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.locusiterator.LocusIterator; import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Collection; import java.util.Iterator; @@ -111,7 +110,9 @@ public class WindowMaker implements Iterable, I this.sourceInfo = shard.getReadProperties(); this.readIterator = new GATKSAMRecordIterator(iterator); - this.libs = new LocusIteratorByState(readIterator,sourceInfo,genomeLocParser,sampleNames); + this.libs = new LocusIteratorByState(readIterator, + sourceInfo.getDownsamplingMethod(), sourceInfo.includeReadsWithDeletionAtLoci(), + sourceInfo.keepUniqueReadListInLIBS(), genomeLocParser,sampleNames); this.sourceIterator = new PeekableIterator(libs); this.intervalIterator = intervals.size()>0 ? new PeekableIterator(intervals.iterator()) : null; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java index c9192e12f..f0e889a63 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.baq; +package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; @@ -31,6 +31,7 @@ import org.broadinstitute.gatk.engine.WalkerManager; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.engine.walkers.BAQMode; import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.baq.BAQ; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java index 59c3f151b..90d8a3fd8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java @@ -26,6 +26,7 @@ package org.broadinstitute.gatk.engine.filters; import org.broadinstitute.gatk.utils.classloader.PluginManager; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.GATKDocUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; @@ -74,6 +75,16 @@ public class FilterManager extends PluginManager { "Please consult the GATK Documentation (" + HelpConstants.GATK_DOCS_URL + ") for more information."); } + /** + * Rather than use the default exception, return a MalformedReadFilterException. + * @param errorMessage error message from formatErrorMessage() + * @return - A MalformedReadFilterException with errorMessage + */ + @Override + protected UserException createMalformedArgumentException(final String errorMessage) { + return new UserException.MalformedReadFilterException(errorMessage); + } + private String userFriendlyListofReadFilters(List> filters) { final String headName = "FilterName", headDoc = "Documentation"; int longestNameLength = -1; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java index 1b59a06d8..6488a857a 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java @@ -29,12 +29,10 @@ import htsjdk.samtools.*; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; import org.broadinstitute.gatk.utils.exceptions.UserException; -import java.util.Collections; - /** * Filter out malformed reads. * diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java index e212bd909..6dd8833b8 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.sam; +package org.broadinstitute.gatk.engine.io; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMProgramRecord; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.HashMap; @@ -41,7 +41,7 @@ import java.util.Map; * User: carneiro * Date: Nov 13 */ -public class BySampleSAMFileWriter extends NWaySAMFileWriter{ +public class BySampleSAMFileWriter extends NWaySAMFileWriter { private final Map sampleToWriterMap; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java index abf70d5a4..011963ecc 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java @@ -23,20 +23,19 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.sam; +package org.broadinstitute.gatk.engine.io; import htsjdk.samtools.*; import htsjdk.samtools.util.ProgressLoggerInterface; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; -import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.broadinstitute.gatk.utils.exceptions.GATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.text.TextFormattingUtils; import java.io.File; -import java.util.Collection; -import java.util.HashMap; -import java.util.Map; +import java.util.*; /** * Created by IntelliJ IDEA. @@ -80,6 +79,79 @@ public class NWaySAMFileWriter implements SAMFileWriter { this(toolkit, ext, order, presorted, indexOnTheFly, generateMD5, null,false); } + /** + * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and sets + * up the writer with the header and presorted status. + * + * @param originalHeader original header + * @param programRecord the program record for this program + */ + public static SAMFileHeader setupWriter(final SAMFileHeader originalHeader, final SAMProgramRecord programRecord) { + final SAMFileHeader header = originalHeader.clone(); + final List oldRecords = header.getProgramRecords(); + final List newRecords = new ArrayList(oldRecords.size()+1); + for ( SAMProgramRecord record : oldRecords ) + if ( (programRecord != null && !record.getId().startsWith(programRecord.getId()))) + newRecords.add(record); + + if (programRecord != null) { + newRecords.add(programRecord); + header.setProgramRecords(newRecords); + } + return header; + } + + /** + * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and returns + * the new header to be added to the BAM writer. + * + * @param toolkit the engine + * @param walker the walker object (so we can extract the command line) + * @param PROGRAM_RECORD_NAME the name for the PG tag + * @return a pre-filled header for the bam writer + */ + public static SAMFileHeader setupWriter(final GenomeAnalysisEngine toolkit, final SAMFileHeader originalHeader, final Object walker, final String PROGRAM_RECORD_NAME) { + final SAMProgramRecord programRecord = createProgramRecord(toolkit, walker, PROGRAM_RECORD_NAME); + return setupWriter(originalHeader, programRecord); + } + + /** + * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and sets + * up the writer with the header and presorted status. + * + * @param writer BAM file writer + * @param toolkit the engine + * @param preSorted whether or not the writer can assume reads are going to be added are already sorted + * @param walker the walker object (so we can extract the command line) + * @param PROGRAM_RECORD_NAME the name for the PG tag + */ + public static void setupWriter(GATKSAMFileWriter writer, GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean preSorted, Object walker, String PROGRAM_RECORD_NAME) { + SAMFileHeader header = setupWriter(toolkit, originalHeader, walker, PROGRAM_RECORD_NAME); + writer.writeHeader(header); + writer.setPresorted(preSorted); + } + + /** + * Creates a program record (@PG) tag + * + * @param toolkit the engine + * @param walker the walker object (so we can extract the command line) + * @param PROGRAM_RECORD_NAME the name for the PG tag + * @return a program record for the tool + */ + public static SAMProgramRecord createProgramRecord(GenomeAnalysisEngine toolkit, Object walker, String PROGRAM_RECORD_NAME) { + final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME); + final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); + try { + final String version = headerInfo.getString("org.broadinstitute.gatk.engine.version"); + programRecord.setProgramVersion(version); + } catch (MissingResourceException e) { + // couldn't care less if the resource is missing... + } + programRecord.setCommandLine(toolkit.createApproximateCommandLineArgumentString(toolkit, walker)); + return programRecord; + } + /** * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved * from toolkit). The in2out map must contain an entry for each input filename and map it @@ -142,7 +214,7 @@ public class NWaySAMFileWriter implements SAMFileWriter { private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord programRecord) { File f = new File(outName); - SAMFileHeader header = Utils.setupWriter(toolkit.getSAMFileHeader(id), programRecord); + SAMFileHeader header = setupWriter(toolkit.getSAMFileHeader(id), programRecord); SAMFileWriterFactory factory = new SAMFileWriterFactory(); factory.setCreateIndex(indexOnTheFly); factory.setCreateMd5File(generateMD5); diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java index c4f776915..a54d2ffac 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java @@ -31,7 +31,7 @@ import htsjdk.tribble.AbstractFeatureReader; import htsjdk.tribble.Feature; import htsjdk.tribble.FeatureCodec; import org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub; -import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager; +import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.bcf2.BCF2Utils; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java index c45432471..dc4824c08 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterArgumentTypeDescriptor.java @@ -28,7 +28,7 @@ package org.broadinstitute.gatk.engine.io.stubs; import htsjdk.samtools.SAMFileWriter; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.OutputStream; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java index cc814e9e6..bc4c0f5d3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMFileWriterStub.java @@ -32,7 +32,7 @@ import htsjdk.samtools.util.ProgressLoggerInterface; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; import org.broadinstitute.gatk.engine.io.OutputTracker; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.utils.baq.BAQ; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; @@ -148,6 +148,27 @@ public class SAMFileWriterStub implements Stub, GATKSAMFileWriter this.samOutputStream = stream; } + /** + * Creates a SAMFileWriter using all of the features currently set in the engine (command line arguments, ReadTransformers, etc) + * @param file the filename to write to + * @param engine the engine + * @return a SAMFileWriter with the correct options set + */ + public static SAMFileWriter createSAMFileWriter(final String file, final GenomeAnalysisEngine engine) { + final SAMFileWriterStub output = new SAMFileWriterStub(engine, new File(file)); + output.processArguments(engine.getArguments()); + return output; + } + + /** + * As {@link #createSAMFileWriter(String, org.broadinstitute.gatk.engine.GenomeAnalysisEngine)}, but also sets the header + */ + public static SAMFileWriter createSAMFileWriter(final String file, final GenomeAnalysisEngine engine, final SAMFileHeader header) { + final SAMFileWriterStub output = (SAMFileWriterStub) createSAMFileWriter(file, engine); + output.writeHeader(header); + return output; + } + /** * Retrieves the SAM file to (ultimately) be created. * @return The SAM file. Must not be null. diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java index 686133922..68163850d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -25,7 +25,6 @@ package org.broadinstitute.gatk.engine.io.stubs; -import htsjdk.tribble.AbstractFeatureReader; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import htsjdk.variant.variantcontext.writer.VariantContextWriter; @@ -136,13 +135,4 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor { return stub; } - - /** - * Returns true if the file will be compressed. - * @param writerFileName Name of the file - * @return true if the file will be compressed. - */ - public static boolean isCompressed(String writerFileName) { - return writerFileName != null && AbstractFeatureReader.hasBlockCompressedExtension(writerFileName); - } } diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java index f40ede581..c9202b03c 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java @@ -30,7 +30,7 @@ import htsjdk.tribble.index.IndexCreator; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; import org.broadinstitute.gatk.engine.io.OutputTracker; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.Options; import htsjdk.variant.variantcontext.writer.VariantContextWriter; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java index cb696e58e..ecce811f9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java @@ -28,6 +28,7 @@ package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.MergingSamRecordIterator; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import java.util.Iterator; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java index 35146f0b8..ea2e081c7 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.sam; +package org.broadinstitute.gatk.engine.iterators; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /** * Checks for and errors out (or fixes if requested) when it detects reads with base qualities that are not encoded with diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java index fa130f930..ca53fcf1d 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java @@ -26,6 +26,7 @@ package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import java.util.Iterator; import java.util.NoSuchElementException; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java index 2eba344bb..a79d592f7 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java @@ -27,6 +27,7 @@ package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; /** * Iterates through a list of elements, tracking the number of elements it has seen. diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java index 492227932..7a3ca935f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java @@ -27,6 +27,7 @@ package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.sam.AlignmentUtils; /** diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java index 18ca02f61..ed5c4b3b9 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java @@ -23,13 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.baq; +package org.broadinstitute.gatk.engine.iterators; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Iterator; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java index a34d4de82..8721779bf 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java @@ -26,8 +26,8 @@ package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import java.util.Iterator; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java index f8126b9a9..3bd174442 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java @@ -33,7 +33,7 @@ import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.utils.Utils; -import org.broadinstitute.gatk.utils.crypt.CryptUtils; +import org.broadinstitute.gatk.engine.crypt.CryptUtils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.io.IOUtils; import org.broadinstitute.gatk.utils.io.Resource; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java index cc41bc5c6..497eafe68 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java index a742ed452..de6500e19 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.recalibration; +package org.broadinstitute.gatk.engine.recalibration; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java index 75666a7e8..a37eb8d88 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java @@ -23,12 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils; +package org.broadinstitute.gatk.engine.samples; import org.broadinstitute.gatk.engine.samples.Sample; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeType; import htsjdk.variant.variantcontext.VariantContext; +import org.broadinstitute.gatk.utils.MathUtils; import java.util.*; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java index 6fdb9fa0a..2744bec61 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java @@ -27,8 +27,8 @@ package org.broadinstitute.gatk.engine.samples; import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.utils.SampleUtils; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.io.File; import java.io.FileNotFoundException; @@ -63,7 +63,7 @@ public class SampleDBBuilder { * Hallucinates sample objects for all the samples in the SAM file and stores them */ public SampleDBBuilder addSamplesFromSAMHeader(final SAMFileHeader header) { - addSamplesFromSampleNames(SampleUtils.getSAMFileSamples(header)); + addSamplesFromSampleNames(ReadUtils.getSAMFileSamples(header)); return this; } diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java index 54c2b873a..ac34b7594 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java @@ -23,16 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.sam; +package org.broadinstitute.gatk.engine.traversals; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.datasources.providers.ShardDataProvider; -import org.broadinstitute.gatk.engine.traversals.TraversalEngine; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.sam.ArtificialPatternedSAMIterator; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /* diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java index d28ea3be4..f84824a59 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.engine.traversals; -import org.broadinstitute.gatk.engine.downsampling.Downsampler; -import org.broadinstitute.gatk.engine.downsampling.ReservoirDownsampler; +import org.broadinstitute.gatk.utils.downsampling.Downsampler; +import org.broadinstitute.gatk.utils.downsampling.ReservoirDownsampler; import org.broadinstitute.gatk.utils.sam.AlignmentStartComparator; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java index 7d93311f2..b3a0603f4 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java @@ -29,15 +29,14 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.datasources.providers.*; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.ActiveRegionTraversalParameters; import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.SampleUtils; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; import org.broadinstitute.gatk.utils.activeregion.ActivityProfile; @@ -49,6 +48,7 @@ import org.broadinstitute.gatk.utils.nanoScheduler.NSReduceFunction; import org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler; import org.broadinstitute.gatk.utils.progressmeter.ProgressMeter; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.io.PrintStream; import java.util.Collection; @@ -162,7 +162,7 @@ public final class TraverseActiveRegions extends TraversalEngine extends Walker allIntervals = new ArrayList(0); for ( IntervalBinding intervalBinding : activeRegionBindings ) { - List intervals = intervalBinding.getIntervals(this.getToolkit()); + List intervals = intervalBinding.getIntervals(this.getToolkit().getGenomeLocParser()); if ( intervals.isEmpty() ) { logger.warn("The interval file " + intervalBinding.getSource() + " contains no intervals that could be parsed."); diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java index c112d7d26..f85123ab6 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java @@ -25,7 +25,7 @@ package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; import java.lang.annotation.*; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java index 96d2d5dad..42398ec33 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java @@ -25,7 +25,7 @@ package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.engine.filters.NotPrimaryAlignmentFilter; import org.broadinstitute.gatk.engine.filters.UnmappedReadFilter; import org.broadinstitute.gatk.utils.GenomeLoc; diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java new file mode 100644 index 000000000..3f8862975 --- /dev/null +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java @@ -0,0 +1,63 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.engine.walkers; + +import htsjdk.samtools.SAMException; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; + +public enum FailMethod { + MAP, + REDUCE, + TREE_REDUCE; + + /** + * Used by QC walkers to test that engine throws appropriate errors. + * Split from the walker in ErrorThrowing.java. + * @param exceptionToThrow Exception type to throw. + */ + public static void fail(final String exceptionToThrow) { + switch (exceptionToThrow) { + case "UserException": + throw new UserException("UserException"); + case "NullPointerException": + throw new NullPointerException(); + case "ReviewedGATKException": + throw new ReviewedGATKException("ReviewedGATKException"); + case "SamError1": + throw new RuntimeException(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_1); + case "SamError2": + throw new RuntimeException(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_2); + case "NoSpace1": + throw new htsjdk.samtools.util.RuntimeIOException(new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)")); + case "NoSpace2": + throw new SAMException("Exception writing BAM index file", new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)")); + default: + throw new UserException.BadArgumentValue("exception", "exception isn't a recognized value " + exceptionToThrow); + } + } +} diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java index 1e7b0e54c..3c6268de3 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java @@ -25,14 +25,14 @@ package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; import org.broadinstitute.gatk.engine.filters.DuplicateReadFilter; import org.broadinstitute.gatk.engine.filters.FailsVendorQualityCheckFilter; import org.broadinstitute.gatk.engine.filters.NotPrimaryAlignmentFilter; import org.broadinstitute.gatk.engine.filters.UnmappedReadFilter; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; /** * Created by IntelliJ IDEA. diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java index 9528cf18e..4ace98d61 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.engine.walkers; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; /** diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java index 31472fdfd..a295bb20f 100644 --- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java +++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java @@ -29,7 +29,7 @@ import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; import org.broadinstitute.gatk.engine.filters.MalformedReadFilter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.engine.samples.Sample; @@ -38,7 +38,7 @@ import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.baq.BAQ; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; -import org.broadinstitute.gatk.utils.recalibration.BQSRMode; +import org.broadinstitute.gatk.engine.recalibration.BQSRMode; import java.util.List; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java index 6596cf324..65605fec3 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java @@ -26,35 +26,23 @@ package org.broadinstitute.gatk.engine; import htsjdk.samtools.*; -import htsjdk.samtools.util.CloseableIterator; import htsjdk.tribble.readers.LineIterator; -import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.commandline.*; -import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.filters.MappingQualityUnavailableFilter; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.walkers.ReadFilters; -import org.broadinstitute.gatk.engine.walkers.ReadWalker; -import org.broadinstitute.gatk.engine.walkers.RodWalker; -import org.broadinstitute.gatk.tools.walkers.qc.ErrorThrowing; -import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.vcf.VCFCodec; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; +import org.broadinstitute.gatk.utils.variant.VCIterable; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -67,7 +55,7 @@ import java.util.*; */ public class EngineFeaturesIntegrationTest extends WalkerTest { private void testBadRODBindingInput(String type, String name, Class c) { - WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variant:variant," + type + " " + WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintVariantsWalker -L 1:1 --variant:variant," + type + " " + b37dbSNP132 + " -R " + b37KGReference + " -o %s", 1, c); executeTest(name, spec); @@ -92,16 +80,16 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { } @Test() private void testMissingBAMnt1() { - testMissingFile("missing BAM", "-T PrintReads -I missing.bam -nt 1"); + testMissingFile("missing BAM", "-T TestPrintReadsWalker -I missing.bam -nt 1"); } @Test() private void testMissingBAMnt4() { - testMissingFile("missing BAM", "-T PrintReads -I missing.bam -nt 4"); + testMissingFile("missing BAM", "-T TestPrintReadsWalker -I missing.bam -nt 4"); } @Test() private void testMissingVCF() { - testMissingFile("missing VCF", "-T SelectVariants -V missing.vcf"); + testMissingFile("missing VCF", "-T TestPrintVariantsWalker -V missing.vcf"); } @Test() private void testMissingInterval() { - testMissingFile("missing interval", "-T PrintReads -L missing.interval_list -I " + b37GoodBAM); + testMissingFile("missing interval", "-T TestPrintReadsWalker -L missing.interval_list -I " + b37GoodBAM); } @@ -127,8 +115,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { @DataProvider(name = "EngineErrorHandlingTestProvider") public Object[][] makeEngineErrorHandlingTestProvider() { - for ( final ErrorThrowing.FailMethod failMethod : ErrorThrowing.FailMethod.values() ) { - if ( failMethod == ErrorThrowing.FailMethod.TREE_REDUCE ) + for ( final FailMethod failMethod : FailMethod.values() ) { + if ( failMethod == FailMethod.TREE_REDUCE ) continue; // cannot reliably throw errors in TREE_REDUCE final String failArg = " -fail " + failMethod.name(); @@ -148,7 +136,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { @Test(enabled = true, dataProvider = "EngineErrorHandlingTestProvider", timeOut = 60 * 1000 ) public void testEngineErrorHandlingTestProvider(final EngineErrorHandlingTestProvider cfg) { for ( int i = 0; i < cfg.iterationsToTest; i++ ) { - final String root = "-T ErrorThrowing -R " + exampleFASTA; + final String root = "-T TestErrorThrowingWalker -R " + exampleFASTA; final String args = root + cfg.args + " -E " + cfg.expectedException.getSimpleName(); WalkerTestSpec spec = new WalkerTestSpec(args, 0, cfg.expectedException); @@ -207,7 +195,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { } private void testBadCompressArgument(final int compress) { - WalkerTestSpec spec = new WalkerTestSpec("-T PrintReads -R " + b37KGReference + " -I " + privateTestDir + "NA12878.1_10mb_2_10mb.bam -o %s -compress " + compress, + WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintReadsWalker -R " + b37KGReference + " -I " + privateTestDir + "NA12878.1_10mb_2_10mb.bam -o %s -compress " + compress, 1, UserException.class); executeTest("badCompress " + compress, spec); } @@ -219,7 +207,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { // -------------------------------------------------------------------------------- @Test(enabled = true) public void testGATKVersionInVCF() throws Exception { - WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -R " + b37KGReference + + WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintVariantsWalker -R " + b37KGReference + " -V " + privateTestDir + "NA12878.WGS.b37.chr20.firstMB.vcf" + " -o %s -L 20:61098", 1, Arrays.asList("")); @@ -229,12 +217,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(vcf))); final VCFHeaderLine versionLine = header.getMetaDataLine(GATKVCFUtils.GATK_COMMAND_LINE_KEY); Assert.assertNotNull(versionLine); - Assert.assertTrue(versionLine.toString().contains("SelectVariants")); + Assert.assertTrue(versionLine.toString().contains("TestPrintVariantsWalker")); } @Test(enabled = true) public void testMultipleGATKVersionsInVCF() throws Exception { - WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -R " + b37KGReference + + WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintVariantsWalker -R " + b37KGReference + " -V " + privateTestDir + "gatkCommandLineInHeader.vcf" + " -o %s", 1, Arrays.asList("")); @@ -244,22 +232,22 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(vcf))); boolean foundHC = false; - boolean foundSV = false; + boolean foundPV = false; for ( final VCFHeaderLine line : header.getMetaDataInInputOrder() ) { if ( line.getKey().equals(GATKVCFUtils.GATK_COMMAND_LINE_KEY) ) { if ( line.toString().contains("HaplotypeCaller") ) { Assert.assertFalse(foundHC); foundHC = true; } - if ( line.toString().contains("SelectVariants") ) { - Assert.assertFalse(foundSV); - foundSV = true; + if ( line.toString().contains("TestPrintVariantsWalker") ) { + Assert.assertFalse(foundPV); + foundPV = true; } } } Assert.assertTrue(foundHC, "Didn't find HaplotypeCaller command line header field"); - Assert.assertTrue(foundSV, "Didn't find SelectVariants command line header field"); + Assert.assertTrue(foundPV, "Didn't find TestPrintVariantsWalker command line header field"); } // -------------------------------------------------------------------------------- @@ -269,7 +257,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { // -------------------------------------------------------------------------------- public WalkerTestSpec testDefaultBaseQualities(final Integer value, final String md5) { - return new WalkerTestSpec("-T PrintReads -R " + b37KGReference + " -I " + privateTestDir + "/baseQualitiesToFix.bam -o %s" + return new WalkerTestSpec("-T TestPrintReadsWalker -R " + b37KGReference + " -I " + privateTestDir + "/baseQualitiesToFix.bam -o %s" + (value != null ? " --defaultBaseQualities " + value : ""), 1, Arrays.asList(md5)); } @@ -297,7 +285,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { @Test public void testGATKEngineConsolidatesCigars() { - final WalkerTestSpec spec = new WalkerTestSpec(" -T PrintReads" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" + " -R " + b37KGReference + " -I " + privateTestDir + "zero_length_cigar_elements.bam" + " -o %s", @@ -327,7 +315,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { final File sampleRenameMapFile = createTestSampleRenameMapFile( Arrays.asList(privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12878.HEADERONLY.bam myNewSampleName")); - final WalkerTestSpec spec = new WalkerTestSpec(" -T PrintReads" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" + " -R " + b37KGReference + " -I " + privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12878.HEADERONLY.bam" + " --sample_rename_mapping_file " + sampleRenameMapFile.getAbsolutePath() + @@ -363,7 +351,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { inputBamReader.close(); } - final WalkerTestSpec spec = new WalkerTestSpec(" -T PrintReads" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" + " -R " + b37KGReference + " -I " + privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12878.HEADERONLY.bam" + " -I " + privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12891.HEADERONLY.bam" + @@ -410,7 +398,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { inputBamReader.close(); } - final WalkerTestSpec spec = new WalkerTestSpec(" -T PrintReads" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" + " -R " + b37KGReference + " -I " + privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12878.HEADERONLY.bam" + " -I " + privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12891.HEADERONLY.bam" + @@ -448,7 +436,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { } inputBamReader.close(); - final WalkerTestSpec spec = new WalkerTestSpec(" -T PrintReads" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" + " -R " + b37KGReference + " -I " + privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12878.HEADERONLY.bam" + " -I " + privateTestDir + "CEUTrio.HiSeq.WGS.b37.READ_GROUP_COLLISIONS_WITH_NA12878.HEADERONLY.bam" + @@ -485,7 +473,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { final File sampleRenameMapFile = createTestSampleRenameMapFile( Arrays.asList(privateTestDir + "CEUTrio.HiSeq.WGS.b37.MERGED.HEADERONLY.bam myNewSampleName")); - final WalkerTestSpec spec = new WalkerTestSpec(" -T PrintReads" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" + " -R " + b37KGReference + " -I " + privateTestDir + "CEUTrio.HiSeq.WGS.b37.MERGED.HEADERONLY.bam" + " --sample_rename_mapping_file " + sampleRenameMapFile.getAbsolutePath() + @@ -519,7 +507,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { final File sampleRenameMapFile = createTestSampleRenameMapFile( Arrays.asList(privateTestDir + "NA12878.WGS.b37.chr20.firstMB.vcf newSampleForNA12878")); - final WalkerTestSpec spec = new WalkerTestSpec(" -T CombineVariants" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintVariantsWalker" + " -R " + b37KGReference + " -V " + privateTestDir + "NA12878.WGS.b37.chr20.firstMB.vcf" + " --sample_rename_mapping_file " + sampleRenameMapFile.getAbsolutePath() + @@ -532,9 +520,9 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { } private void verifySampleRenaming( final File outputVCF, final String newSampleName ) throws IOException { - final Pair> headerAndVCIter = GATKVCFUtils.readAllVCs(outputVCF, new VCFCodec()); + final Pair> headerAndVCIter = VCIterable.readAllVCs(outputVCF, new VCFCodec()); final VCFHeader header = headerAndVCIter.getFirst(); - final GATKVCFUtils.VCIterable iter = headerAndVCIter.getSecond(); + final VCIterable iter = headerAndVCIter.getSecond(); // Verify that sample renaming occurred at both the header and record levels (checking only the first 10 records): @@ -572,7 +560,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { final File sampleRenameMapFile = createTestSampleRenameMapFile( Arrays.asList(privateTestDir + "vcf/vcfWithGenotypes.vcf badSample")); - final WalkerTestSpec spec = new WalkerTestSpec(" -T CombineVariants" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintVariantsWalker" + " -R " + b37KGReference + " -V " + privateTestDir + "vcf/vcfWithGenotypes.vcf" + " --sample_rename_mapping_file " + sampleRenameMapFile.getAbsolutePath() + @@ -588,7 +576,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { final File sampleRenameMapFile = createTestSampleRenameMapFile( Arrays.asList(privateTestDir + "vcf/vcfWithoutGenotypes.vcf badSample")); - final WalkerTestSpec spec = new WalkerTestSpec(" -T CombineVariants" + + final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintVariantsWalker" + " -R " + b37KGReference + " -V " + privateTestDir + "vcf/vcfWithoutGenotypes.vcf" + " --sample_rename_mapping_file " + sampleRenameMapFile.getAbsolutePath() + @@ -675,7 +663,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { //Returns the output file private File testBAMFeatures(final String args, final String md5) { - WalkerTestSpec spec = new WalkerTestSpec("-T PrintReads -R " + b37KGReference + + WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintReadsWalker -R " + b37KGReference + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam" + " --no_pg_tag -o %s " + args, 1, Arrays.asList(".bam"), Arrays.asList(md5)); @@ -708,16 +696,34 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { "BAM index was created even though it was disabled"); } - private void testVCFFeatures(final String args, final String md5) { - WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -R " + b37KGReference + + @DataProvider(name = "vcfFeaturesData") + public Object[][] getVCFFeaturesData() { + return new Object[][]{ + {"--sites_only", "94bf1f2c0946e933515e4322323a5716"}, + {"--bcf", "03f2d6988f54a332da48803c78f9c4b3"} + }; + } + + @Test(dataProvider = "vcfFeaturesData") + public void testVCFFeatures(final String args, final String md5) { + WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintVariantsWalker -R " + b37KGReference + " -V " + privateTestDir + "CEUtrioTest.vcf" + " --no_cmdline_in_header -o %s " + args, 1, Arrays.asList(md5)); executeTest("testVCFFeatures: "+args, spec); } - private void testVCFFormatHandling(final boolean writeFullFormat, final String md5) { - WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -R " + b37KGReference + + @DataProvider(name = "vcfFormatHandlingData") + public Object[][] getVCFFormatHandlingData() { + return new Object[][]{ + {true, "95b6262efbd40b6b72f44f808f3e4c45"}, + {false, "333232e08b8cdd3303309e438c44277f"} + }; + } + + @Test(dataProvider = "vcfFormatHandlingData") + public void testVCFFormatHandling(final boolean writeFullFormat, final String md5) { + WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintVariantsWalker -R " + b37KGReference + " -V " + privateTestDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf" + " --no_cmdline_in_header -o %s " + " --fullyDecode " //Without this parameter, the FORMAT fields will be emitted unchanged. Oops @@ -725,12 +731,4 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { 1, Arrays.asList(md5)); executeTest("testVCFFormatHandling: "+(writeFullFormat ? "Untrimmed" : "Trimmed"), spec); } - - @Test - public void testVCFWriterFeatures() { - testVCFFeatures("--sites_only", "94bf1f2c0946e933515e4322323a5716"); - testVCFFeatures("--bcf", "03f2d6988f54a332da48803c78f9c4b3"); - testVCFFormatHandling(true, "2b0fa660b0cef4b0f45a10febb453b6c"); - testVCFFormatHandling(false, "5960311fdd9ee6db88587efaaf4055a0"); - } -} \ No newline at end of file +} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java index ab547b7c1..cd8b19bd0 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java @@ -23,21 +23,21 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.variant; +package org.broadinstitute.gatk.engine; import htsjdk.tribble.index.DynamicIndexCreator; import htsjdk.tribble.index.IndexCreator; import htsjdk.tribble.index.interval.IntervalIndexCreator; import htsjdk.tribble.index.linear.LinearIndexCreator; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.Walker; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; +import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java index ff60ae30c..424083a11 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java @@ -25,14 +25,13 @@ package org.broadinstitute.gatk.engine; +import org.broadinstitute.gatk.engine.walkers.TestCountReadsWalker; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.Tags; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.engine.walkers.Walker; -import org.broadinstitute.gatk.tools.walkers.qc.CountReads; -import org.broadinstitute.gatk.tools.walkers.readutils.PrintReads; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.GenomeLocSortedSet; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -55,7 +54,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest { @Test(expectedExceptions=UserException.class) public void testEmptySamFileListHandling() throws Exception { GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine(); - testEngine.setWalker(new CountReads()); //generalizable to any walker requiring reads + testEngine.setWalker(new TestCountReadsWalker()); //generalizable to any walker requiring reads //supply command line args so validateSuppliedReads() knows whether reads were passed in GATKArgumentCollection testArgs = new GATKArgumentCollection(); @@ -115,7 +114,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest { GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine(); - testEngine.setWalker(new PrintReads()); + testEngine.setWalker(new TestCountReadsWalker()); testEngine.setIntervals(new GenomeLocSortedSet(genomeLocParser)); testEngine.validateSuppliedIntervals(); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java new file mode 100644 index 000000000..4c6e35d0c --- /dev/null +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java @@ -0,0 +1,37 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.engine; + +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.commandline.Hidden; + +@Hidden +public class InstantiableWalker extends Walker { + // Public constructor will generate instantiable message + public InstantiableWalker() {} + public Long reduceInit() { return 0L; } + public Long reduce(Integer value, Long accum) { return 0L; } +} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java index 27b6c1ca3..2d48487e4 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.engine; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.LocusWalker; import org.broadinstitute.gatk.utils.SimpleTimer; import org.testng.Assert; @@ -104,7 +104,7 @@ public class MaxRuntimeIntegrationTest extends WalkerTest { @Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 120 * 1000) public void testMaxRuntime(final MaxRuntimeTestProvider cfg) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T PrintReads -R " + hg18Reference + "-T TestPrintReadsWalker -R " + hg18Reference + " -I " + validationDataLocation + "NA12878.WEx.downsampled20x.bam -o /dev/null" + " -maxRuntime " + cfg.maxRuntime + " -maxRuntimeUnits " + cfg.unit, 0, Collections.emptyList()); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java index 1153bccb8..dcc58ea36 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java @@ -29,9 +29,9 @@ import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.*; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.ValidationExclusion; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.datasources.providers.LocusShardDataProvider; import org.broadinstitute.gatk.engine.datasources.providers.ReadShardDataProvider; import org.broadinstitute.gatk.engine.datasources.reads.*; @@ -39,14 +39,13 @@ import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource import org.broadinstitute.gatk.engine.executive.WindowMaker; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.engine.traversals.*; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.GenomeLocSortedSet; -import org.broadinstitute.gatk.utils.SampleUtils; import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; @@ -196,7 +195,7 @@ public class ReadMetricsUnitTest extends BaseTest { false, (byte)30, false, true, null, IntervalMergingRule.ALL); engine.setReadsDataSource(dataSource); - final Set samples = SampleUtils.getSAMFileSamples(dataSource.getHeader()); + final Set samples = ReadUtils.getSAMFileSamples(dataSource.getHeader()); final TraverseLociNano traverseLociNano = new TraverseLociNano(1); final DummyLocusWalker walker = new DummyLocusWalker(); @@ -237,7 +236,7 @@ public class ReadMetricsUnitTest extends BaseTest { false, (byte)30, false, true, null, IntervalMergingRule.ALL); engine.setReadsDataSource(dataSource); - final Set samples = SampleUtils.getSAMFileSamples(dataSource.getHeader()); + final Set samples = ReadUtils.getSAMFileSamples(dataSource.getHeader()); final List intervals = new ArrayList<>(contigs.size()); for ( final String contig : contigs ) diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java index d11c4bf57..7de5f0dbf 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java @@ -23,14 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils; +package org.broadinstitute.gatk.engine; -import org.apache.commons.io.FileUtils; -import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.broadinstitute.gatk.utils.io.IOUtils; -import org.testng.Assert; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.BaseTest; -import org.testng.annotations.DataProvider; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.io.File; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java new file mode 100644 index 000000000..11a3c3d6d --- /dev/null +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java @@ -0,0 +1,37 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.engine; + +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.commandline.Hidden; + +@Hidden +public class UninstantiableWalker extends Walker { + // Private constructor will generate uninstantiable message + private UninstantiableWalker() {} + public Long reduceInit() { return 0L; } + public Long reduce(Integer value, Long accum) { return 0L; } +} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java index 62348ef19..0a940ef22 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java @@ -25,9 +25,7 @@ package org.broadinstitute.gatk.engine; -import org.broadinstitute.gatk.utils.commandline.Hidden; import org.broadinstitute.gatk.engine.walkers.Walker; -import org.broadinstitute.gatk.tools.walkers.qc.CountLoci; import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.Assert; @@ -47,8 +45,8 @@ public class WalkerManagerUnitTest { @Test public void testPresentWalker() { - Walker countLociWalker = walkerManager.createByName("CountLoci"); - Assert.assertEquals(CountLoci.class,countLociWalker.getClass()); + Walker instantiableWalker = walkerManager.createByName("InstantiableWalker"); + Assert.assertEquals(InstantiableWalker.class, instantiableWalker.getClass()); } @Test(expectedExceptions=UserException.class) @@ -61,11 +59,3 @@ public class WalkerManagerUnitTest { walkerManager.createByName("UninstantiableWalker"); } } - -@Hidden -class UninstantiableWalker extends Walker { - // Private constructor will generate uninstantiable message - private UninstantiableWalker() {} - public Long reduceInit() { return 0L; } - public Long reduce(Integer value, Long accum) { return 0L; } -} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java index 8d8f7d261..1229ecfff 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.interval; +package org.broadinstitute.gatk.engine.arguments; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.testng.annotations.Test; @@ -40,7 +40,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testAllImplicitIntervalParsing() { String md5 = "7821db9e14d4f8e07029ff1959cd5a99"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s", @@ -54,7 +54,7 @@ public class IntervalIntegrationTest extends WalkerTest { // public void testAllExplicitIntervalParsing() { // String md5 = "7821db9e14d4f8e07029ff1959cd5a99"; // WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( -// "-T CountLoci" + +// "-T TestCountLociWalker" + // " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + // " -R " + hg18Reference + // " -L all" + @@ -67,7 +67,7 @@ public class IntervalIntegrationTest extends WalkerTest { @Test public void testUnmappedReadInclusion() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T PrintReads" + + "-T TestPrintReadsWalker" + " -I " + validationDataLocation + "MV1994.bam" + " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" + " -L unmapped" + @@ -87,7 +87,7 @@ public class IntervalIntegrationTest extends WalkerTest { @Test public void testMixedMappedAndUnmapped() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T PrintReads" + + "-T TestPrintReadsWalker" + " -I " + validationDataLocation + "MV1994.bam" + " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" + " -L Escherichia_coli_K12:4630000-4639675" + @@ -109,7 +109,7 @@ public class IntervalIntegrationTest extends WalkerTest { @Test(enabled = false) public void testUnmappedReadExclusion() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T PrintReads" + + "-T TestPrintReadsWalker" + " -I " + validationDataLocation + "MV1994.bam" + " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" + " -XL unmapped" + @@ -130,7 +130,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testIntervalParsingFromFile() { String md5 = "48a24b70a0b376535542b996af517398"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -144,7 +144,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testIntervalMergingFromFiles() { String md5 = "9ae0ea9e3c9c6e1b9b6252c8395efdc1"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -159,7 +159,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testIntervalExclusionsFromFiles() { String md5 = "26ab0db90d72e28ad0ba1e22ee510510"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -174,7 +174,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testMixedIntervalMerging() { String md5 = "7c5aba41f53293b712fd86d08ed5b36e"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -189,7 +189,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testBed() { String md5 = "cf4278314ef8e4b996e1b798d8eb92cf"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -203,7 +203,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testComplexVCF() { String md5 = "166d77ac1b46a1ec38aa35ab7e628ab5"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -217,7 +217,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testComplexVCFWithPadding() { String md5 = "649ee93d50739c656e94ec88a32c7ffe"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " --interval_padding 2" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + @@ -232,7 +232,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testMergingWithComplexVCF() { String md5 = "6d7fce9fee471194aa8b5b6e47267f03"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -247,7 +247,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testEmptyVCF() { String md5 = "897316929176464ebc9ad085f31e7284"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -261,7 +261,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testIncludeExcludeIsTheSame() { String md5 = "897316929176464ebc9ad085f31e7284"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" + " -R " + hg18Reference + " -o %s" + @@ -276,7 +276,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testSymbolicAlleles() { String md5 = "52745056d2fd5904857bbd4984c08098"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci" + + "-T TestCountLociWalker" + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam" + " -R " + b36KGReference + " -o %s" + @@ -290,7 +290,7 @@ public class IntervalIntegrationTest extends WalkerTest { public void testIntersectionOfLexicographicallySortedIntervals() { final String md5 = "18be9375e5a753f766616a51eb6131f0"; WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - " -T CountLoci" + + " -T TestCountLociWalker" + " -I " + privateTestDir + "NA12878.4.snippet.bam" + " -R " + b37KGReference + " -L " + privateTestDir + "lexicographicallySortedIntervals.bed" + diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java index 8ab2159d6..ca9682747 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java @@ -23,44 +23,33 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.commandline; +package org.broadinstitute.gatk.engine.arguments; -import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.broadinstitute.gatk.utils.exceptions.UserException; - import org.testng.annotations.Test; -import org.testng.annotations.DataProvider; -/** - * Created by IntelliJ IDEA. - * User: chartl - * Date: 8/31/12 - * Time: 11:03 AM - * To change this template use File | Settings | File Templates. - */ public class InvalidArgumentIntegrationTest extends WalkerTest { - private static final String callsB36 = BaseTest.validationDataLocation + "lowpass.N3.chr1.raw.vcf"; - - private WalkerTest.WalkerTestSpec baseTest(String flag, String arg, Class exeption) { - return new WalkerTest.WalkerTestSpec("-T VariantsToTable -M 10 --variant:vcf " - + callsB36 + " -F POS,CHROM -R " - + b36KGReference + " -o %s " + flag + " " + arg, - 1, exeption); - - } - @Test public void testUnknownReadFilter() { - executeTest("UnknownReadFilter",baseTest("-rf","TestUnknownReadFilter", UserException.MalformedReadFilterException.class)); + executeTest("UnknownReadFilter", + new WalkerTest.WalkerTestSpec( + " -T TestPrintReadsWalker" + + " -R " + exampleFASTA + + " -I " + publicTestDir + "exampleBAM.bam" + + " -o %s" + + " -rf TestUnknownReadFilter", + 1, UserException.MalformedReadFilterException.class)); } @Test public void testMalformedWalkerArgs() { executeTest("MalformedWalkerArgs", - new WalkerTest.WalkerTestSpec("-T UnknownWalkerName -M 10 --variant:vcf " - + callsB36 + " -F POS,CHROM -R " - + b36KGReference + " -o %s ", + new WalkerTest.WalkerTestSpec( + " -T UnknownWalkerName" + + " -R " + exampleFASTA + + " -I " + publicTestDir + "exampleBAM.bam" + + " -o %s", 1, UserException.MalformedWalkerArgumentsException.class)); } } diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java index d690f681c..73c177688 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.commandline; +package org.broadinstitute.gatk.engine.arguments; import java.io.File; import java.io.IOException; @@ -58,7 +58,7 @@ public class LoggingIntegrationTest { super(LoggingTestProvider.class); // TODO: a better command line that exercises log levels besides INFO - this.baseCmdLine = String.format("java -cp %s %s -T SelectVariants -R %s -V %s -L 1:1000000-2000000 --no_cmdline_in_header", + this.baseCmdLine = String.format("java -cp %s %s -T TestPrintVariantsWalker -R %s -V %s -L 1:1000000-2000000 --no_cmdline_in_header", StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar), CommandLineGATK.class.getCanonicalName(), BaseTest.b37KGReference, BaseTest.b37_NA12878_OMNI); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java index c44bfdc03..beac3ace8 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java @@ -23,8 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.crypt; +package org.broadinstitute.gatk.engine.crypt; +import org.broadinstitute.gatk.engine.crypt.CryptUtils; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java index 9cafd61a7..350ba7b75 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.crypt; +package org.broadinstitute.gatk.engine.crypt; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; @@ -35,7 +35,7 @@ import java.util.Arrays; public class GATKKeyIntegrationTest extends WalkerTest { - public static final String BASE_COMMAND = String.format("-T PrintReads -R %s -I %s -o %%s", + public static final String BASE_COMMAND = String.format("-T TestPrintReadsWalker -R %s -I %s -o %%s", publicTestDir + "exampleFASTA.fasta", publicTestDir + "exampleBAM.bam"); public static final String MD5_UPON_SUCCESSFUL_RUN = "e7b4a5b62f9d4badef1cd07040011b2b"; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java index 5fd6475ce..89ef0b26e 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.crypt; +package org.broadinstitute.gatk.engine.crypt; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java index f9d9dfe53..99d7559c4 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java @@ -29,7 +29,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import java.util.List; /** diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java index 8914a4876..6665b7481 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java @@ -29,8 +29,7 @@ package org.broadinstitute.gatk.engine.datasources.providers; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import java.util.List; /** diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java index 29ccbd644..f77b6613a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java @@ -31,10 +31,10 @@ import htsjdk.tribble.BasicFeature; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.RodBinding; -import org.broadinstitute.gatk.engine.refdata.RODRecordListImpl; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.RODRecordListImpl; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.Utils; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java index 5eb9c7ac7..3f620f900 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java @@ -32,7 +32,7 @@ import org.testng.annotations.Test; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard; import org.broadinstitute.gatk.engine.iterators.GenomeLocusIterator; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import htsjdk.samtools.reference.ReferenceSequence; import htsjdk.samtools.util.StringUtil; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java index 650b14690..8b476e6ef 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java @@ -30,12 +30,12 @@ import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.*; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.broadinstitute.gatk.engine.datasources.reads.Shard; import org.broadinstitute.gatk.engine.executive.WindowMaker; import org.broadinstitute.gatk.engine.datasources.reads.LocusShard; import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java index fdec85870..dbc2f5518 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java @@ -30,14 +30,14 @@ import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.utils.commandline.Tags; import org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; import org.testng.Assert; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.engine.datasources.reads.Shard; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.codecs.table.TableFeature; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet.RMDStorageType; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet.RMDStorageType; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java index f1ee6ab78..258e61b49 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java @@ -33,6 +33,7 @@ import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java index 27c287c9c..7df9bc2cb 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java @@ -27,7 +27,7 @@ package org.broadinstitute.gatk.engine.datasources.reads; import com.google.caliper.Param; import org.broadinstitute.gatk.engine.WalkerManager; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.engine.walkers.LocusWalker; /** diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java index e35f1d592..a54237bfb 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java @@ -33,6 +33,7 @@ import org.broadinstitute.gatk.utils.commandline.Tags; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java index 30eaeb6a1..aa66d6636 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java @@ -26,22 +26,22 @@ package org.broadinstitute.gatk.engine.datasources.reads; import com.google.caliper.Param; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.Tags; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.filters.UnmappedReadFilter; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; -import org.broadinstitute.gatk.engine.walkers.ReadWalker; -import org.broadinstitute.gatk.engine.walkers.Walker; -import org.broadinstitute.gatk.tools.walkers.qc.CountLoci; -import org.broadinstitute.gatk.tools.walkers.qc.CountReads; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; import org.broadinstitute.gatk.utils.classloader.JVMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import java.io.File; +import java.io.PrintStream; import java.util.Collections; /** @@ -100,7 +100,7 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark { private enum WalkerType { COUNT_READS { @Override - Walker create() { return new CountReads(); } + Walker create() { return new CountReadsPerformanceWalker(); } }, COUNT_BASES_IN_READ { @Override @@ -109,8 +109,8 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark { COUNT_LOCI { @Override Walker create() { - CountLoci walker = new CountLoci(); - JVMUtils.setFieldValue(JVMUtils.findField(CountLoci.class,"out"),walker,System.out); + CountLociPerformanceWalker walker = new CountLociPerformanceWalker(); + JVMUtils.setFieldValue(JVMUtils.findField(CountLociPerformanceWalker.class,"out"),walker,System.out); return walker; } }; @@ -118,6 +118,21 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark { } } +class CountLociPerformanceWalker extends TestCountLociWalker { + // NOTE: Added this output during porting. Previous version of test was reaching out of engine + // and into production o.b.g.tools.walkers.qc.CountLoci. + @Output + PrintStream out; + + @Override + public void onTraversalDone(Long result) { + out.println(result); + } +} + +class CountReadsPerformanceWalker extends TestCountReadsWalker { +} + class CountBasesInReadPerformanceWalker extends ReadWalker { private long As; private long Cs; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java index eb3c89493..896549adf 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java @@ -25,11 +25,9 @@ package org.broadinstitute.gatk.engine.datasources.reads; -import org.broadinstitute.gatk.engine.datasources.reads.LocusShard; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; import org.broadinstitute.gatk.utils.GenomeLocParser; import java.util.List; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java index be48194b5..3836409b9 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java @@ -26,9 +26,9 @@ package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.*; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.utils.ValidationExclusion; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.utils.BaseTest; @@ -36,6 +36,7 @@ import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.commandline.Tags; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java index 526b8ce02..eb1915f0c 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java @@ -29,16 +29,17 @@ import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.*; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.testng.annotations.AfterMethod; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java index bb1cd7521..c975fb166 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java @@ -27,6 +27,7 @@ package org.broadinstitute.gatk.engine.datasources.reads; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.Tags; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java index 46a4cb5f1..a544d716a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java @@ -43,7 +43,7 @@ public class ReferenceDataSourceIntegrationTest extends WalkerTest { Assert.assertTrue(dictFile.createNewFile()); final WalkerTestSpec spec = new WalkerTestSpec( - " -T PrintReads" + + " -T TestPrintReadsWalker" + " -R " + dummyReference.getAbsolutePath() + " -I " + privateTestDir + "NA12878.4.snippet.bam" + " -o %s", @@ -62,7 +62,7 @@ public class ReferenceDataSourceIntegrationTest extends WalkerTest { Assert.assertTrue(faiFile.createNewFile()); final WalkerTestSpec spec = new WalkerTestSpec( - " -T PrintReads" + + " -T TestPrintReadsWalker" + " -R " + dummyReference.getAbsolutePath() + " -I " + privateTestDir + "NA12878.4.snippet.bam" + " -o %s", diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java index baa2af098..a77c0961c 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java @@ -26,13 +26,13 @@ package org.broadinstitute.gatk.engine.datasources.rmd; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder; import org.testng.Assert; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.codecs.table.TableFeature; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet.RMDStorageType; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet.RMDStorageType; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java index 6c403cd83..514b85737 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java @@ -29,7 +29,7 @@ import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.refdata.utils.*; +import org.broadinstitute.gatk.utils.refdata.utils.*; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java index 2f171de0b..c98243adc 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java @@ -26,6 +26,7 @@ package org.broadinstitute.gatk.engine.downsampling; import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; @@ -34,7 +35,7 @@ public class DownsamplingIntegrationTest extends WalkerTest { @Test public void testDetectLowDcovValueWithLocusTraversal() { final WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T CountLoci -R " + publicTestDir + "exampleFASTA.fasta -I " + publicTestDir + "exampleBAM.bam -o %s " + + "-T TestCountLociWalker -R " + publicTestDir + "exampleFASTA.fasta -I " + publicTestDir + "exampleBAM.bam -o %s " + "-dcov " + (DownsamplingMethod.MINIMUM_SAFE_COVERAGE_TARGET_FOR_LOCUS_BASED_TRAVERSALS - 1), 1, UserException.class diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java index 19eec62cf..27804c6d1 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java @@ -29,7 +29,9 @@ import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingReadsIterator; +import org.broadinstitute.gatk.utils.downsampling.SimplePositionalDownsampler; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream; import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStreamAnalyzer; @@ -97,7 +99,7 @@ public class DownsamplingReadsIteratorUnitTest extends BaseTest { int minDistanceBetweenStacks = 1; int maxDistanceBetweenStacks = maxReadLength + 1; - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); // brute force testing! for ( int numContigs : Arrays.asList(1, 2, 5) ) { @@ -133,7 +135,7 @@ public class DownsamplingReadsIteratorUnitTest extends BaseTest { public void runDownsamplingReadsIteratorTest( DownsamplingReadsIteratorTest test ) { logger.warn("Running test: " + test); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); test.run(); } } diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java index 918537439..8e3ac5f49 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java @@ -28,7 +28,9 @@ package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.downsampling.FractionalDownsampler; +import org.broadinstitute.gatk.utils.downsampling.ReadsDownsampler; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -106,7 +108,7 @@ public class FractionalDownsamplerUnitTest extends BaseTest { public void runFractionalDownsamplerTest( FractionalDownsamplerTest test ) { logger.warn("Running test: " + test); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); ReadsDownsampler downsampler = new FractionalDownsampler(test.fraction); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java index 2544b72fd..74a936782 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java @@ -26,7 +26,9 @@ package org.broadinstitute.gatk.engine.downsampling; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.downsampling.Downsampler; +import org.broadinstitute.gatk.utils.downsampling.LevelingDownsampler; import org.testng.annotations.Test; import org.testng.annotations.DataProvider; import org.testng.Assert; @@ -106,7 +108,7 @@ public class LevelingDownsamplerUnitTest extends BaseTest { public void testLevelingDownsamplerWithUniformStacks( LevelingDownsamplerUniformStacksTest test ) { logger.warn("Running test: " + test); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); Downsampler> downsampler = new LevelingDownsampler, Object>(test.targetSize); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java index 2606a01d3..fdc8587ba 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java @@ -29,8 +29,11 @@ import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.downsampling.PerSampleDownsamplingReadsIterator; +import org.broadinstitute.gatk.utils.downsampling.ReadsDownsamplerFactory; +import org.broadinstitute.gatk.utils.downsampling.SimplePositionalDownsamplerFactory; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.engine.iterators.VerifyingSamIterator; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; @@ -194,7 +197,7 @@ public class PerSampleDownsamplingReadsIteratorUnitTest extends BaseTest { int thisSampleNumContigs = MathUtils.randomIntegerInRange(minContigs, maxContigs); int thisSampleStacksPerContig = MathUtils.randomIntegerInRange(streamStacksPerContig.minStacksPerContig, streamStacksPerContig.maxStacksPerContig); - int thisSampleNumUnmappedReads = GenomeAnalysisEngine.getRandomGenerator().nextDouble() < unmappedReadsFraction ? unmappedReadsCount : 0; + int thisSampleNumUnmappedReads = Utils.getRandomGenerator().nextDouble() < unmappedReadsFraction ? unmappedReadsCount : 0; ArtificialSingleSampleReadStream thisSampleStream = new ArtificialSingleSampleReadStream(header, readGroupID, @@ -252,7 +255,7 @@ public class PerSampleDownsamplingReadsIteratorUnitTest extends BaseTest { @DataProvider(name = "PerSampleDownsamplingReadsIteratorTestDataProvider") public Object[][] createPerSampleDownsamplingReadsIteratorTests() { - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); // Some values don't vary across tests int targetCoverage = PerSampleDownsamplingReadsIteratorTest.StreamStackDepth.UNIFORM_MEDIUM.minReadsPerStack; @@ -293,7 +296,7 @@ public class PerSampleDownsamplingReadsIteratorUnitTest extends BaseTest { public void runPerSampleDownsamplingReadsIteratorTest( PerSampleDownsamplingReadsIteratorTest test ) { logger.warn("Running test: " + test); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); test.run(); } } diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java index 4e6f157f1..88a1c5d5c 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java @@ -28,7 +28,9 @@ package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.downsampling.ReadsDownsampler; +import org.broadinstitute.gatk.utils.downsampling.ReservoirDownsampler; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -85,7 +87,7 @@ public class ReservoirDownsamplerUnitTest extends BaseTest { public void testReservoirDownsampler( ReservoirDownsamplerTest test ) { logger.warn("Running test: " + test); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); ReadsDownsampler downsampler = new ReservoirDownsampler(test.reservoirSize); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java index e04c347b3..c22a3eaed 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java @@ -28,7 +28,9 @@ package org.broadinstitute.gatk.engine.downsampling; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.downsampling.ReadsDownsampler; +import org.broadinstitute.gatk.utils.downsampling.SimplePositionalDownsampler; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.annotations.DataProvider; @@ -102,14 +104,14 @@ public class SimplePositionalDownsamplerUnitTest extends BaseTest { @DataProvider(name = "SimplePositionalDownsamplerTestDataProvider") public Object[][] createSimplePositionalDownsamplerTestData() { - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); for ( int targetCoverage = 1; targetCoverage <= 10000; targetCoverage *= 10 ) { for ( int contigs = 1; contigs <= 2; contigs++ ) { for ( int numStacks = 0; numStacks <= 10; numStacks++ ) { List stackSizes = new ArrayList(numStacks); for ( int stack = 1; stack <= numStacks; stack++ ) { - stackSizes.add(GenomeAnalysisEngine.getRandomGenerator().nextInt(targetCoverage * 2) + 1); + stackSizes.add(Utils.getRandomGenerator().nextInt(targetCoverage * 2) + 1); } new SimplePositionalDownsamplerTest(targetCoverage, stackSizes, contigs > 1); } @@ -123,7 +125,7 @@ public class SimplePositionalDownsamplerUnitTest extends BaseTest { public void testSimplePostionalDownsampler( SimplePositionalDownsamplerTest test ) { logger.warn("Running test: " + test); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); ReadsDownsampler downsampler = new SimplePositionalDownsampler(test.targetCoverage); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java index 7a0122085..d3fb18896 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java @@ -27,7 +27,7 @@ package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java index 3ff8ed4dc..f4232067d 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java @@ -35,7 +35,7 @@ public class BadReadGroupsIntegrationTest extends WalkerTest { @Test public void testMissingReadGroup() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T PrintReads -R " + b36KGReference + " -I " + privateTestDir + "missingReadGroup.bam -o /dev/null", + "-T TestPrintReadsWalker -R " + b36KGReference + " -I " + privateTestDir + "missingReadGroup.bam -o /dev/null", 0, UserException.ReadMissingReadGroup.class); executeTest("test Missing Read Group", spec); @@ -44,7 +44,7 @@ public class BadReadGroupsIntegrationTest extends WalkerTest { @Test public void testUndefinedReadGroup() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T PrintReads -R " + b36KGReference + " -I " + privateTestDir + "undefinedReadGroup.bam -o /dev/null", + "-T TestPrintReadsWalker -R " + b36KGReference + " -I " + privateTestDir + "undefinedReadGroup.bam -o /dev/null", 0, UserException.ReadHasUndefinedReadGroup.class); executeTest("test Undefined Read Group", spec); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java index d25db50e0..20566f510 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java @@ -31,7 +31,7 @@ import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java index 0f61de248..4e801815f 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java @@ -27,10 +27,10 @@ package org.broadinstitute.gatk.engine.filters; import htsjdk.samtools.*; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java index a00f0a0ba..343ad656e 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.gatk.engine.filters; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.ValidationExclusion; import java.util.Collections; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java index 1dfffa359..60e529281 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.commandline; +package org.broadinstitute.gatk.engine.io.stubs; import htsjdk.variant.variantcontext.VariantContext; import it.unimi.dsi.fastutil.objects.ObjectArrayList; import htsjdk.samtools.SAMFileWriter; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.io.stubs.*; +import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import org.testng.Assert; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java index 7c3aca2d1..b295e1230 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java @@ -30,10 +30,9 @@ import static org.testng.Assert.fail; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.reference.ReferenceSequenceFile; -import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.testng.Assert; -import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java index 6cbd4fd1b..fc7465de3 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java @@ -29,6 +29,9 @@ import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.gatk.utils.BaseTest; import static org.testng.Assert.assertEquals; + +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIteratorAdapter; import org.testng.annotations.Test; import java.util.Iterator; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java index 207e01ab9..994de2b28 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java @@ -23,12 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.sam; +package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.SAMFileHeader; +import org.broadinstitute.gatk.engine.iterators.MisencodedBaseQualityReadTransformer; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java index c926d066c..d6f4be97a 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java @@ -27,6 +27,8 @@ package org.broadinstitute.gatk.engine.iterators; import htsjdk.samtools.*; import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIteratorAdapter; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java index 371f94f00..c7e7d05d5 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java @@ -30,6 +30,7 @@ import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIteratorAdapter; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java index d7b9b3dda..3042e3082 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java @@ -25,22 +25,19 @@ package org.broadinstitute.gatk.engine.phonehome; +import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker; -import org.broadinstitute.gatk.engine.walkers.Walker; -import org.broadinstitute.gatk.tools.walkers.qc.CountLoci; -import org.broadinstitute.gatk.tools.walkers.qc.CountRODs; -import org.broadinstitute.gatk.tools.walkers.qc.CountReads; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.jets3t.service.S3Service; import org.jets3t.service.S3ServiceException; import org.jets3t.service.ServiceException; @@ -72,7 +69,7 @@ public class GATKRunReportUnitTest extends BaseTest { @BeforeClass public void setup() throws Exception { - walker = new CountReads(); + walker = new RunReportDummyReadWalker(); exception = new IllegalArgumentException("javaException"); engine = new GenomeAnalysisEngine(); engine.setArguments(new GATKArgumentCollection()); @@ -109,9 +106,9 @@ public class GATKRunReportUnitTest extends BaseTest { public Object[][] makeGATKReportCreationTest() { List tests = new ArrayList(); - final Walker readWalker = new CountReads(); - final Walker lociWalker = new CountLoci(); - final Walker rodWalker = new CountRODs(); + final Walker readWalker = new RunReportDummyReadWalker(); + final Walker lociWalker = new RunReportDummyLocusWalker(); + final Walker rodWalker = new RunReportDummyRodWalker(); final Walker artWalker = new RunReportDummyActiveRegionWalker(); final Exception noException = null; @@ -286,6 +283,57 @@ public class GATKRunReportUnitTest extends BaseTest { } } + class RunReportDummyReadWalker extends ReadWalker { + @Override + public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) { + return 0; + } + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(Integer value, Integer sum) { + return 0; + } + } + + class RunReportDummyLocusWalker extends LocusWalker { + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + return 0; + } + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(Integer value, Integer sum) { + return 0; + } + } + + class RunReportDummyRodWalker extends RodWalker { + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + return 0; + } + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(Integer value, Integer sum) { + return 0; + } + } + class RunReportDummyActiveRegionWalker extends ActiveRegionWalker { @Override public ActivityProfileState isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java index e1d81b587..b32a3db63 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.engine.traversals; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocSortedSet; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java index 50eb49664..b8b9c75f1 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java @@ -28,14 +28,13 @@ package org.broadinstitute.gatk.engine.traversals; import com.google.java.contract.PreconditionError; import htsjdk.samtools.*; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.engine.datasources.reads.*; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.utils.GenomeLocSortedSet; -import org.broadinstitute.gatk.utils.SampleUtils; import org.broadinstitute.gatk.utils.activeregion.ActiveRegionReadState; import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; import org.broadinstitute.gatk.utils.interval.IntervalUtils; @@ -482,7 +481,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest { false, (byte)30, false, true, null, IntervalMergingRule.ALL); engine.setReadsDataSource(dataSource); - final Set samples = SampleUtils.getSAMFileSamples(dataSource.getHeader()); + final Set samples = ReadUtils.getSAMFileSamples(dataSource.getHeader()); traverseActiveRegions.initialize(engine, walker); List providers = new ArrayList(); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java index 70336a26d..3e6b3f2f4 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java @@ -27,6 +27,7 @@ package org.broadinstitute.gatk.engine.traversals; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.reference.ReferenceSequenceFile; +import org.broadinstitute.gatk.engine.walkers.TestCountReadsWalker; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.Tags; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; @@ -35,10 +36,10 @@ import org.broadinstitute.gatk.engine.datasources.reads.*; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; import org.broadinstitute.gatk.engine.walkers.ReadWalker; -import org.broadinstitute.gatk.tools.walkers.qc.CountReads; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; @@ -128,7 +129,7 @@ public class TraverseReadsUnitTest extends BaseTest { bamList = new ArrayList(); bamList.add(bam); - countReadWalker = new CountReads(); + countReadWalker = new TestCountReadsWalker(); traversalEngine = new TraverseReadsNano(1); traversalEngine.initialize(engine, countReadWalker); diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java new file mode 100644 index 000000000..8b7a8d758 --- /dev/null +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java @@ -0,0 +1,58 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.engine.walkers; + +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; + +import java.io.PrintStream; + +public class TestCountLociWalker extends LocusWalker { + @Output + private PrintStream out; + + @Override + public Integer map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { + return 1; + } + + @Override + public Long reduceInit() { + return 0L; + } + + @Override + public Long reduce(final Integer value, final Long sum) { + return value + sum; + } + + @Override + public void onTraversalDone(final Long result) { + out.println(result); + } +} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java new file mode 100644 index 000000000..cc0162fc1 --- /dev/null +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java @@ -0,0 +1,59 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.engine.walkers; + +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; + +import java.io.PrintStream; + +public class TestCountReadsWalker extends ReadWalker { + @Output + PrintStream out; + + @Override + public Integer map(final ReferenceContext ref, final GATKSAMRecord read, final RefMetaDataTracker metaDataTracker) { + return 1; + } + + @Override + public Long reduceInit() { + return 0L; + } + + @Override + public Long reduce(final Integer value, final Long sum) { + return value + sum; + } + + @Override + public void onTraversalDone(final Long result) { + if (out != null) + out.println(result); + } +} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java new file mode 100644 index 000000000..00774f7b7 --- /dev/null +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java @@ -0,0 +1,70 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.engine.walkers; + +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; + +public class TestErrorThrowingWalker extends RefWalker implements TreeReducible, NanoSchedulable { + @Input(fullName = "exception", shortName = "E", doc = "Java class of exception to throw", required = true) + public String exceptionToThrow; + + @Argument(fullName = "failMethod", shortName = "fail", doc = "Determines which method to fail in", required = false) + public FailMethod failMethod = FailMethod.MAP; + + @Override + public Integer map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { + if (ref == null) // only throw exception when we are in proper map, not special map(null) call + return null; + + if (failMethod == FailMethod.MAP) + FailMethod.fail(exceptionToThrow); + + return 0; + } + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(final Integer value, final Integer sum) { + if (value != null && failMethod == FailMethod.REDUCE) + FailMethod.fail(exceptionToThrow); + return sum; + } + + @Override + public Integer treeReduce(final Integer lhs, final Integer rhs) { + if (failMethod == FailMethod.TREE_REDUCE) + FailMethod.fail(exceptionToThrow); + return rhs; + } +} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java new file mode 100644 index 000000000..bbf653ac1 --- /dev/null +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java @@ -0,0 +1,76 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.engine.walkers; + +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileWriter; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.io.NWaySAMFileWriter; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; + +public class TestPrintReadsWalker extends ReadWalker implements NanoSchedulable { + @Output + private GATKSAMFileWriter out; + + @Argument(fullName = "no_pg_tag", shortName = "npt", doc ="", required = false) + public boolean NO_PG_TAG = false; + + @Override + public void initialize() { + // All for the no_pg_tag. Should this be in the engine and not in the walker? + final GenomeAnalysisEngine toolkit = getToolkit(); + final SAMFileHeader outputHeader = toolkit.getSAMFileHeader().clone(); + final String PROGRAM_RECORD_NAME = "GATK PrintReads"; + final boolean preSorted = true; + if (toolkit.getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) { + NWaySAMFileWriter.setupWriter(out, toolkit, outputHeader, preSorted, this, PROGRAM_RECORD_NAME); + } else { + out.writeHeader(outputHeader); + out.setPresorted(preSorted); + } + } + + @Override + public GATKSAMRecord map(final ReferenceContext ref, final GATKSAMRecord read, final RefMetaDataTracker metaDataTracker) { + return read; + } + + @Override + public SAMFileWriter reduceInit() { + return out; + } + + @Override + public SAMFileWriter reduce(final GATKSAMRecord read, final SAMFileWriter output) { + output.addAlignment(read); + return output; + } +} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java new file mode 100644 index 000000000..8af514693 --- /dev/null +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java @@ -0,0 +1,99 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.engine.walkers; + +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; +import org.broadinstitute.gatk.engine.GATKVCFUtils; +import org.broadinstitute.gatk.engine.SampleUtils; +import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.variant.ChromosomeCountConstants; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; + +import java.util.*; + +public class TestPrintVariantsWalker extends RodWalker implements TreeReducible { + @ArgumentCollection + private StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + + @Argument(fullName = "fullyDecode", doc = "If true, the incoming VariantContext will be fully decoded", required = false) + private boolean fullyDecode = false; + + @Output + private VariantContextWriter vcfWriter = null; + + private Map vcfRods = null; + + @Override + public void initialize() { + vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()); + final Set samples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); + final Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); + headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions)); + headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); + final VCFHeader vcfHeader = new VCFHeader(headerLines, samples); + vcfWriter.writeHeader(vcfHeader); + } + + @Override + public Integer map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { + if (tracker == null) + return 0; + final Collection vcs = tracker.getValues(variantCollection.variants, context.getLocation()); + for (VariantContext vc : vcs) { + if (fullyDecode) + vc = vc.fullyDecode(vcfRods.get(vc.getSource()), getToolkit().lenientVCFProcessing()); + vcfWriter.add(vc); + } + return vcs.isEmpty() ? 0 : 1; + } + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(final Integer counter, final Integer sum) { + return counter + sum; + } + + @Override + public Integer treeReduce(final Integer lhs, final Integer rhs) { + return reduce(lhs, rhs); + } + + @Override + public void onTraversalDone(final Integer sum) { + } +} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java index a4c896e74..ff6b1242f 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java @@ -33,7 +33,7 @@ import htsjdk.variant.vcf.VCFCodec; import org.apache.commons.lang.StringUtils; import org.broadinstitute.gatk.engine.CommandLineExecutable; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.crypt.CryptUtils; import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.MD5DB; @@ -54,6 +54,8 @@ import java.text.SimpleDateFormat; import java.util.*; public class WalkerTest extends BaseTest { + public static final String gatkKeyFile = CryptUtils.GATK_USER_KEY_DIRECTORY + "gsamembers_broadinstitute.org.key"; + private static final boolean GENERATE_SHADOW_BCF = true; private static final boolean ENABLE_PHONE_HOME_FOR_TESTS = false; private static final boolean ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX = false; @@ -64,7 +66,7 @@ public class WalkerTest extends BaseTest { @BeforeMethod public void initializeWalkerTests() { logger.debug("Initializing walker tests"); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); } @AfterSuite diff --git a/public/gatk-queue-extensions-generator/pom.xml b/public/gatk-queue-extensions-generator/pom.xml index d1c75c578..9799191a8 100644 --- a/public/gatk-queue-extensions-generator/pom.xml +++ b/public/gatk-queue-extensions-generator/pom.xml @@ -21,7 +21,7 @@ ${project.groupId} - gatk-tools-public + gatk-engine ${project.version} diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java index 1e9e5cc45..1a6cda658 100644 --- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java @@ -507,7 +507,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { @Override protected String getFreezeFields() { return String.format( ("if (%2$s != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(%2$s))%n" + - " if (!org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor.isCompressed(%2$s.getPath))%n" + + " if (!org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.isCompressed(%2$s.getPath))%n" + " %1$s = new File(%2$s.getPath + \"%3$s\")%n"), auxFieldName, originalFieldName, Tribble.STANDARD_INDEX_EXTENSION); } diff --git a/public/gatk-queue-extensions-public/pom.xml b/public/gatk-queue-extensions-public/pom.xml index a48c3e6e1..b2d833d50 100644 --- a/public/gatk-queue-extensions-public/pom.xml +++ b/public/gatk-queue-extensions-public/pom.xml @@ -39,6 +39,10 @@ log4j log4j + + picard + picard + ${project.groupId} - gatk-tools-public + gatk-utils ${project.version} test-jar test diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala index 36031d948..f116af51a 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala @@ -32,6 +32,7 @@ import org.broadinstitute.gatk.utils.commandline.Input import org.broadinstitute.gatk.utils.commandline.Output import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction import org.broadinstitute.gatk.queue.extensions.gatk.{TaggedFile, VcfGatherFunction, LocusScatterFunction} +import org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.isCompressed class MuTect extends org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK with ScatterGatherableFunction { analysisName = "MuTect" @@ -409,7 +410,7 @@ class MuTect extends org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGA override def freezeFieldValues() { super.freezeFieldValues() if (vcf != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(vcf)) - if (!org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor.isCompressed(vcf.getPath)) + if (!org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.isCompressed(vcf.getPath)) vcfIndex = new File(vcf.getPath + ".idx") dbsnpIndexes ++= dbsnp.filter(orig => orig != null).map(orig => new File(orig.getPath + ".idx")) cosmicIndexes ++= cosmic.filter(orig => orig != null).map(orig => new File(orig.getPath + ".idx")) diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala index fd54be631..0bedbf543 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala @@ -27,7 +27,6 @@ package org.broadinstitute.gatk.queue.extensions.gatk import java.io.{PrintStream, PrintWriter, File} import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction -import org.broadinstitute.gatk.engine.downsampling.DownsampleType import org.broadinstitute.gatk.utils.commandline.{Input, Gather, Output} import org.broadinstitute.gatk.queue.function.{InProcessFunction, CommandLineFunction} import org.broadinstitute.gatk.tools.walkers.coverage.CoverageUtils @@ -35,6 +34,7 @@ import scala.collection.JavaConversions._ import scala.Some import org.broadinstitute.gatk.utils.text.XReadLines import org.broadinstitute.gatk.queue.util.VCF_BAM_utilities +import org.broadinstitute.gatk.utils.downsampling.DownsampleType // Minimal refactor from a package object to a file full of classes/objects // due to ongoing bugs with inner classes/objects in package objects: diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala index 0e568b61f..c1d71e281 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala @@ -59,7 +59,7 @@ case class GATKIntervals(reference: File, intervals: Seq[File], intervalsString: this.excludeIntervalsString.map(GATKIntervals.createBinding(_, "excludeIntervalsString")) IntervalUtils.parseIntervalBindings( - referenceDataSource, + referenceDataSource.getReference, includeIntervalBindings, intervalSetRule, intervalMergingRule, intervalPadding.getOrElse(0), excludeIntervalBindings).toList diff --git a/public/gatk-queue/pom.xml b/public/gatk-queue/pom.xml index be329a738..525f0b59a 100644 --- a/public/gatk-queue/pom.xml +++ b/public/gatk-queue/pom.xml @@ -21,7 +21,7 @@ ${project.groupId} - gatk-tools-public + gatk-utils ${project.version} @@ -47,7 +47,7 @@ ${project.groupId} - gatk-tools-public + gatk-utils ${project.version} test-jar test diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala index be5a17f43..ddc11eb34 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala @@ -26,8 +26,8 @@ package org.broadinstitute.gatk.queue.util import org.broadinstitute.gatk.queue.function.QFunction -import org.broadinstitute.gatk.engine.report.GATKReportTable import org.broadinstitute.gatk.queue.engine.JobRunInfo +import org.broadinstitute.gatk.utils.report.GATKReportTable /** * A mixin to add Job info to the class diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala index b3b0b33c8..082062364 100644 --- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala +++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala @@ -30,9 +30,10 @@ import org.broadinstitute.gatk.utils.io.{Resource} import org.broadinstitute.gatk.queue.engine.{JobRunInfo, QGraph} import org.broadinstitute.gatk.queue.function.QFunction import org.broadinstitute.gatk.utils.R.{RScriptLibrary, RScriptExecutor} -import org.broadinstitute.gatk.engine.report.{GATKReportTable, GATKReport} +import org.broadinstitute.gatk.utils.report.GATKReportTable import org.broadinstitute.gatk.utils.exceptions.UserException import org.apache.commons.io.{FileUtils, IOUtils} +import org.broadinstitute.gatk.utils.report.{GATKReportTable, GATKReport} /** * Writes out RunInfo to a GATKReport diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala index 62ac8e1fe..5cd25eb0c 100644 --- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala +++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala @@ -35,9 +35,9 @@ import org.broadinstitute.gatk.utils.MD5DB import org.broadinstitute.gatk.queue.{QScript, QCommandLine} import org.broadinstitute.gatk.queue.util.Logging import java.io.{FilenameFilter, File} -import org.broadinstitute.gatk.engine.report.GATKReport import org.apache.commons.io.FileUtils import org.apache.commons.io.filefilter.WildcardFileFilter +import org.broadinstitute.gatk.utils.report.GATKReport object QueueTest extends BaseTest with Logging { diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml index 7dbb397af..36f2b2256 100644 --- a/public/gatk-root/pom.xml +++ b/public/gatk-root/pom.xml @@ -130,6 +130,12 @@ reflections 0.9.9-RC1 + + + org.slf4j + slf4j-api + 1.6.1 + org.slf4j slf4j-log4j12 @@ -404,6 +410,7 @@ ${gatk.basedir} diff true + ${gatk.queuetests.run} ${java.io.tmpdir} @@ -458,8 +465,7 @@ ${gatk.basedir} diff true - - ${gatk.queuetests.run} + ${gatk.queuetests.run} ${java.io.tmpdir} diff --git a/public/gatk-tools-public/pom.xml b/public/gatk-tools-public/pom.xml index 709817355..0a5755026 100644 --- a/public/gatk-tools-public/pom.xml +++ b/public/gatk-tools-public/pom.xml @@ -24,6 +24,26 @@ gatk-engine ${project.version} + + org.apache.commons + commons-jexl + + + + ${project.groupId} + gatk-utils + ${project.version} + test-jar + test + + + + ${project.groupId} + gatk-engine + ${project.version} + test-jar + test + com.google.caliper diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java index 43403ab79..99ce0af6d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java @@ -40,7 +40,7 @@ import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.text.XReadLines; import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.bcf2.BCF2Codec; import org.broadinstitute.gatk.utils.collections.Pair; import htsjdk.variant.vcf.VCFCodec; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java index 72d30defd..4bc91d6e3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java @@ -27,9 +27,9 @@ package org.broadinstitute.gatk.tools; import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotationHelpUtils; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.help.HelpUtils; /** * Utility program to print a list of available annotations @@ -66,7 +66,7 @@ public class ListAnnotations extends CommandLineProgram { @Override protected int execute() throws Exception { - HelpUtils.listAnnotations(); + AnnotationHelpUtils.listAnnotations(); return 0; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java index 9127b5ee2..20240897c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java @@ -32,9 +32,9 @@ import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.MathUtils; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java index 9f5ee9c55..c5670068d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java @@ -32,9 +32,9 @@ import htsjdk.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java index 44579f9ba..0fefa4350 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java index 05054a3f3..c76b2917d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java index cf1323fe6..2fdfdfe6d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java index 544feb784..9cb6eeeaa 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java index f514f67f0..e41f9d4b5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java @@ -28,15 +28,15 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.Utils; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.exceptions.UserException; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java index 042ba487f..c0371647a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java @@ -30,17 +30,17 @@ import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotationHelpUtils; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.help.HelpUtils; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.BaseUtils; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; @@ -206,7 +206,7 @@ public class VariantAnnotator extends RodWalker implements Ann public void initialize() { if ( LIST ) { - HelpUtils.listAnnotations(); + AnnotationHelpUtils.listAnnotations(); System.exit(0); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java index 60c882417..dac0d7174 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java @@ -30,9 +30,9 @@ import com.google.java.contract.Requires; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.commandline.RodBinding; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java index 03f707f9d..e7e0b5431 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java @@ -26,7 +26,7 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import org.broadinstitute.gatk.utils.commandline.RodBinding; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import htsjdk.variant.variantcontext.Allele; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java index 1011a4935..d8e3c8c3c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java @@ -23,21 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.help; +package org.broadinstitute.gatk.tools.walkers.annotator.interfaces; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotationType; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.gatk.utils.classloader.PluginManager; import java.util.List; -/** - * NON-javadoc/doclet help-related utility methods should go here. Anything with a com.sun.javadoc.* dependency - * should go into DocletUtils for use only by doclets. - */ -public class HelpUtils { +public class AnnotationHelpUtils { /** * Simple method to print a list of available annotations. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java index a6a81d758..41c2650ca 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator.interfaces; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.variantcontext.Genotype; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java index 55a30d8be..571055524 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.annotator.interfaces; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java index 726ea9ba4..1c59dc51d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java @@ -28,15 +28,15 @@ package org.broadinstitute.gatk.tools.walkers.beagle; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java index dab5d160e..7e08defd4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java @@ -25,21 +25,21 @@ package org.broadinstitute.gatk.tools.walkers.beagle; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.samples.Gender; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.tools.walkers.variantrecalibration.VQSRCalibrationCurve; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.MathUtils; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFFilterHeaderLine; import htsjdk.variant.vcf.VCFHeader; @@ -278,7 +278,7 @@ public class ProduceBeagleInput extends RodWalker { log10Likelihoods = genotype.getLikelihoods().getAsVector(); // see if we need to randomly mask out genotype in this position. - if ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() <= insertedNoCallRate ) { + if ( Utils.getRandomGenerator().nextDouble() <= insertedNoCallRate ) { // we are masking out this genotype log10Likelihoods = isMaleOnChrX ? HAPLOID_FLAT_LOG10_LIKELIHOODS : DIPLOID_FLAT_LOG10_LIKELIHOODS; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java index c45ceb269..939a52ad0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java @@ -30,17 +30,17 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.Allele; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java index 1757e7bc0..332486b1a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java @@ -29,9 +29,9 @@ import org.broadinstitute.gatk.utils.commandline.Advanced; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.By; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.LocusWalker; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java index 9ab8555cd..0c94747b3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java @@ -31,9 +31,9 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java index 7514fa5a8..e71860794 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java @@ -27,7 +27,7 @@ package org.broadinstitute.gatk.tools.walkers.coverage; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java index 3fc2e597a..20c480901 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java @@ -27,23 +27,20 @@ package org.broadinstitute.gatk.tools.walkers.coverage; import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.gatk.engine.walkers.*; -import org.broadinstitute.gatk.utils.commandline.Advanced; -import org.broadinstitute.gatk.utils.commandline.Argument; -import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.SeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.SeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.SampleUtils; import org.broadinstitute.gatk.utils.codecs.refseq.RefSeqCodec; import org.broadinstitute.gatk.utils.codecs.refseq.RefSeqFeature; import org.broadinstitute.gatk.utils.collections.Pair; @@ -51,6 +48,7 @@ import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.io.File; import java.io.PrintStream; @@ -336,7 +334,7 @@ public class DepthOfCoverage extends LocusWalker getSamplesFromToolKit(DoCOutputType.Partition type) { HashSet partition = new HashSet(); if ( type == DoCOutputType.Partition.sample ) { - partition.addAll(SampleUtils.getSAMFileSamples(getToolkit())); + partition.addAll(ReadUtils.getSAMFileSamples(getToolkit().getSAMFileHeader())); } else if ( type == DoCOutputType.Partition.readgroup ) { for ( SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups() ) { partition.add(rg.getSample()+"_rg_"+rg.getReadGroupId()); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java index a23cfe36b..a793ed07d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.tools.walkers.coverage; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.collections.Pair; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java index 370cea281..e596cdd70 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java @@ -35,9 +35,9 @@ import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java index 910afa4d6..b0b18abc6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java @@ -28,11 +28,11 @@ package org.broadinstitute.gatk.tools.walkers.diagnostics; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.engine.walkers.LocusWalker; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.QualityUtils; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java index e9856de0d..ba4542768 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java @@ -29,10 +29,10 @@ import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.utils.Median; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java index a632f252e..438b38e36 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java @@ -28,10 +28,10 @@ package org.broadinstitute.gatk.tools.walkers.diagnostics; import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java index 80fca6787..e026b286b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java @@ -27,9 +27,9 @@ package org.broadinstitute.gatk.tools.walkers.examples; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Hidden; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java index 8cfc14e41..bdddc5040 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.tools.walkers.examples; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.LocusWalker; import org.broadinstitute.gatk.engine.walkers.TreeReducible; import org.broadinstitute.gatk.utils.genotyper.DiploidGenotype; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java index 8fd41524f..c6e451cd2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java @@ -31,13 +31,13 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java index 8459506ba..562f00bf4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.tools.walkers.fasta; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RefWalker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.collections.Pair; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java index 22a592b77..e5178dd74 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java @@ -27,9 +27,9 @@ package org.broadinstitute.gatk.tools.walkers.fasta; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RefWalker; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java index 513763b68..c5302b9a2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java @@ -25,7 +25,7 @@ package org.broadinstitute.gatk.tools.walkers.filters; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java index 3988498c0..33009b5b6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java @@ -29,16 +29,16 @@ import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.Window; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java new file mode 100644 index 000000000..831655f56 --- /dev/null +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java @@ -0,0 +1,64 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.help; + +import com.sun.javadoc.RootDoc; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.tools.walkers.qc.DocumentationTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeatureHandler; +import org.broadinstitute.gatk.utils.help.GATKDoclet; + +import java.io.IOException; +import java.util.Arrays; +import java.util.List; + +/** + * GATKDocs for walkers. + * Specifically, allows testing of documentation. + */ +public class WalkerDoclet extends GATKDoclet { + /** + * Any class that's in this list will be included in the documentation + * when the -test argument is provided. Useful for debugging. + */ + private static final List> testOnlyKeepers = Arrays.asList( + DocumentationTest.class, CommandLineGATK.class, UserException.class); + + @Override + protected List> getTestOnlyKeepers() { + return testOnlyKeepers; + } + + @Override + protected DocumentedGATKFeatureHandler createDocumentedGATKFeatureHandler() { + return new WalkerDocumentationHandler(); + } + + public static boolean start(RootDoc rootDoc) throws IOException { + return new WalkerDoclet().startProcessDocs(rootDoc); + } +} diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java new file mode 100644 index 000000000..bd31f09d8 --- /dev/null +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java @@ -0,0 +1,345 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.help; + +import org.apache.commons.lang.StringUtils; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; +import org.broadinstitute.gatk.utils.help.GATKDocUtils; +import org.broadinstitute.gatk.utils.help.GenericDocumentationHandler; +import org.broadinstitute.gatk.utils.help.HelpConstants; + +import java.lang.annotation.Annotation; +import java.lang.reflect.InvocationTargetException; +import java.lang.reflect.Method; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Map; + +public class WalkerDocumentationHandler extends GenericDocumentationHandler { + private final static String CMDLINE_GATK_URL = HelpConstants.GATK_DOCS_URL + "org_broadinstitute_gatk_engine_CommandLineGATK.php"; + + @Override + protected CommandLineProgram createCommandLineProgram() { + return new CommandLineGATK(); + } + + /** + * Umbrella function that groups the collection of values for specific annotations applied to an + * instance of class c. Lists of collected values are added directly to the "toProcess" object. + * Requires being able to instantiate the class. + * + * @param classToProcess the object to instantiate and query for the annotation + * @param root the root of the document handler, to which we'll store collected annotations + */ + @Override + protected void getClazzAnnotations(Class classToProcess, Map root) { + // + // attempt to instantiate the class + final Object instance = makeInstanceIfPossible(classToProcess); + if (instance != null) { + final Class myClass = instance.getClass(); + // Get parallelism options + final HashSet> parallelOptions = getParallelism(myClass, new HashSet>()); + root.put("parallel", parallelOptions); + // Get annotation info (what type of annotation, standard etc.) + final HashSet annotInfo = getAnnotInfo(myClass, new HashSet()); + root.put("annotinfo", StringUtils.join(annotInfo, ", ")); + // Get annotation field (whether it goes in INFO or FORMAT) + root.put("annotfield", getAnnotField(myClass)); + // Get walker type if applicable + root.put("walkertype", getWalkerType(myClass)); + // Get partition type if applicable + root.put("partitiontype", getPartitionType(myClass)); + // Get read filter annotations (ReadFilters) if applicable + final HashSet> bucket= getReadFilters(myClass, new HashSet>()); + root.put("readfilters", bucket); + // Get default downsampling settings + final HashMap dsSettings = getDownSamplingSettings(myClass, new HashMap()); + root.put("downsampling", dsSettings); + // Get reference window size settings + final HashMap refwindow = getRefWindow(myClass, new HashMap()); + root.put("refwindow", refwindow); + // Get ActiveRegion size settings + final HashMap activeRegion = getActiveRegion(myClass, new HashMap()); + root.put("activeregion", activeRegion); + // Get annotation header line description if applicable + final Object annotDescriptLines = getAnnotDescript(instance, myClass); + root.put("annotdescript", annotDescriptLines); + + // anything else? + } else { + // put empty items to avoid blowups + root.put("parallel", new HashSet()); + root.put("annotinfo", ""); + root.put("annotfield", ""); + root.put("walkertype", ""); + root.put("partitiontype", ""); + root.put("readfilters", new HashSet>()); + root.put("downsampling", new HashMap()); + root.put("refwindow", new HashMap()); + root.put("activeregion", new HashMap()); + root.put("annotdescript", new ArrayList>()); + } + } + + /** + * Utility function that looks up annotation descriptions if applicable. + * + * @param myClass the class to query + * @return a hash map of descriptions, otherwise an empty map + */ + private Object getAnnotDescript(Object instance, Class myClass) { + // + // Check if the class has the method we want + for (Method classMethod : myClass.getMethods()) { + if (classMethod.toString().contains("getDescriptions") && classMethod.toString().contains("annotator")) { + try { + return classMethod.invoke(instance); + } catch (IllegalArgumentException e) { + } catch (IllegalAccessException e) { + } catch (InvocationTargetException e) { + } + } + } + return null; + } + + /** + * Utility function that checks which parallelism options are available for an instance of class c. + * + * @param myClass the class to query for the interfaces + * @param parallelOptions an empty HashSet in which to collect the info + * @return a hash set of parallelism options, otherwise an empty set + */ + private HashSet> getParallelism(Class myClass, HashSet> parallelOptions) { + // + // Retrieve interfaces + Class[] implementedInterfaces = myClass.getInterfaces(); + for (Class intfClass : implementedInterfaces) { + final HashMap nugget = new HashMap(); + if (intfClass.getSimpleName().equals("TreeReducible")) { + nugget.put("name", intfClass.getSimpleName()); + nugget.put("arg", HelpConstants.ARG_TREEREDUCIBLE); + nugget.put("link", CMDLINE_GATK_URL + "#" + HelpConstants.ARG_TREEREDUCIBLE); + } else if (intfClass.getSimpleName().equals("NanoSchedulable")) { + nugget.put("name", intfClass.getSimpleName()); + nugget.put("arg", HelpConstants.ARG_NANOSCHEDULABLE); + nugget.put("link", CMDLINE_GATK_URL + "#" + HelpConstants.ARG_NANOSCHEDULABLE); + } else { + continue; + } + parallelOptions.add(nugget); + } + // Look up superclasses recursively + final Class mySuperClass = myClass.getSuperclass(); + if (mySuperClass.getSimpleName().equals("Object")) { + return parallelOptions; + } + return getParallelism(mySuperClass, parallelOptions); + } + + /** + * Utility function that looks up whether the annotation goes in INFO or FORMAT field. + * + * @param myClass the class to query for the interfaces + * @return a String specifying the annotation field + */ + private final String getAnnotField(Class myClass) { + // + // Look up superclasses recursively until we find either + // GenotypeAnnotation or InfoFieldAnnotation + final Class mySuperClass = myClass.getSuperclass(); + if (mySuperClass == InfoFieldAnnotation.class) { + return "INFO (variant-level)"; + } else if (mySuperClass == GenotypeAnnotation.class) { + return "FORMAT (sample genotype-level)"; + } else if (mySuperClass.getSimpleName().equals("Object")) { + return ""; + } + return getAnnotField(mySuperClass); + } + + /** + * Utility function that determines the annotation type for an instance of class c. + * + * @param myClass the class to query for the interfaces + * @param annotInfo an empty HashSet in which to collect the info + * @return a hash set of the annotation types, otherwise an empty set + */ + private HashSet getAnnotInfo(Class myClass, HashSet annotInfo) { + // + // Retrieve interfaces + Class[] implementedInterfaces = myClass.getInterfaces(); + for (Class intfClass : implementedInterfaces) { + if (intfClass.getName().contains("Annotation")) { + annotInfo.add(intfClass.getSimpleName()); + } + } + // Look up superclasses recursively + final Class mySuperClass = myClass.getSuperclass(); + if (mySuperClass.getSimpleName().equals("Object")) { + return annotInfo; + } + return getAnnotInfo(mySuperClass, annotInfo); + } + + /** + * Utility function that determines the default downsampling settings for an instance of class c. + * + * @param myClass the class to query for the settings + * @param dsSettings an empty HashMap in which to collect the info + * @return a hash set of the downsampling settings, otherwise an empty set + */ + private HashMap getDownSamplingSettings(Class myClass, HashMap dsSettings) { + // + // Retrieve annotation + if (myClass.isAnnotationPresent(Downsample.class)) { + final Annotation thisAnnotation = myClass.getAnnotation(Downsample.class); + if(thisAnnotation instanceof Downsample) { + final Downsample dsAnnotation = (Downsample) thisAnnotation; + dsSettings.put("by", dsAnnotation.by().toString()); + dsSettings.put("to_cov", dsAnnotation.toCoverage()); + } + } + return dsSettings; + } + + /** + * Utility function that determines the reference window size for an instance of class c. + * + * @param myClass the class to query for the settings + * @param refWindow an empty HashMap in which to collect the info + * @return a HashMap of the window start and stop, otherwise an empty HashMap + */ + private HashMap getRefWindow(Class myClass, HashMap refWindow) { + // + // Retrieve annotation + if (myClass.isAnnotationPresent(Reference.class)) { + final Annotation thisAnnotation = myClass.getAnnotation(Reference.class); + if(thisAnnotation instanceof Reference) { + final Reference refAnnotation = (Reference) thisAnnotation; + refWindow.put("start", refAnnotation.window().start()); + refWindow.put("stop", refAnnotation.window().stop()); + } + } + return refWindow; + } + + /** + * Utility function that determines the ActiveRegion settings for an instance of class c. + * + * @param myClass the class to query for the settings + * @param activeRegion an empty HashMap in which to collect the info + * @return a HashMap of the ActiveRegion parameters, otherwise an empty HashMap + */ + private HashMap getActiveRegion(Class myClass, HashMap activeRegion) { + // + // Retrieve annotation + if (myClass.isAnnotationPresent(ActiveRegionTraversalParameters.class)) { + final Annotation thisAnnotation = myClass.getAnnotation(ActiveRegionTraversalParameters.class); + if(thisAnnotation instanceof ActiveRegionTraversalParameters) { + final ActiveRegionTraversalParameters arAnnotation = (ActiveRegionTraversalParameters) thisAnnotation; + activeRegion.put("ext", arAnnotation.extension()); + activeRegion.put("max", arAnnotation.maxRegion()); + activeRegion.put("min", arAnnotation.minRegion()); + } + } + return activeRegion; + } + + /** + * Utility function that determines the partition type of an instance of class c. + * + * @param myClass the class to query for the annotation + * @return the partition type if applicable, otherwise an empty string + */ + private String getPartitionType(Class myClass) { + // + // Retrieve annotation + if (myClass.isAnnotationPresent(PartitionBy.class)) { + final Annotation thisAnnotation = myClass.getAnnotation(PartitionBy.class); + if(thisAnnotation instanceof PartitionBy) { + final PartitionBy partAnnotation = (PartitionBy) thisAnnotation; + return partAnnotation.value().toString(); + } + } + return ""; + } + + /** + * Utility function that determines the type of walker subclassed by an instance of class c. + * + * @param myClass the class to query for the annotation + * @return the type of walker if applicable, otherwise an empty string + */ + private String getWalkerType(Class myClass) { + // + // Look up superclasses recursively until we find either Walker or Object + final Class mySuperClass = myClass.getSuperclass(); + if (mySuperClass.getSimpleName().equals("Walker")) { + return myClass.getSimpleName(); + } else if (mySuperClass.getSimpleName().equals("Object")) { + return ""; + } + return getWalkerType(mySuperClass); + } + + /** + * Utility function that finds the values of ReadFilters annotation applied to an instance of class c. + * + * @param myClass the class to query for the annotation + * @param bucket a container in which we store the annotations collected + * @return a hash set of values, otherwise an empty set + */ + private HashSet> getReadFilters(Class myClass, HashSet> bucket) { + // + // Retrieve annotation + if (myClass.isAnnotationPresent(ReadFilters.class)) { + final Annotation thisAnnotation = myClass.getAnnotation(ReadFilters.class); + if(thisAnnotation instanceof ReadFilters) { + final ReadFilters rfAnnotation = (ReadFilters) thisAnnotation; + for (Class filter : rfAnnotation.value()) { + // make hashmap of simplename and url + final HashMap nugget = new HashMap(); + nugget.put("name", filter.getSimpleName()); + nugget.put("filename", GATKDocUtils.phpFilenameForClass(filter)); + bucket.add(nugget); + } + } + } + // Look up superclasses recursively + final Class mySuperClass = myClass.getSuperclass(); + if (mySuperClass.getSimpleName().equals("Object")) { + return bucket; + } + return getReadFilters(mySuperClass, bucket); + } +} diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java index a3848dccc..fd876991f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java @@ -30,9 +30,9 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.LocusWalker; import org.broadinstitute.gatk.engine.walkers.Requires; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java index 1500ce37d..8ba387ca5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java @@ -26,8 +26,8 @@ package org.broadinstitute.gatk.tools.walkers.qc; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.engine.walkers.Requires; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java index 221c4a9a2..096ce70dc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java @@ -31,9 +31,9 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RefWalker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.collections.Pair; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java index 51c161731..5987199b1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java @@ -27,9 +27,9 @@ package org.broadinstitute.gatk.tools.walkers.qc; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.LocusWalker; import org.broadinstitute.gatk.engine.walkers.NanoSchedulable; import org.broadinstitute.gatk.engine.walkers.TreeReducible; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java index d665e618e..293cfd0ed 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java @@ -27,8 +27,8 @@ package org.broadinstitute.gatk.tools.walkers.qc; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.samples.Gender; import org.broadinstitute.gatk.engine.samples.Sample; import org.broadinstitute.gatk.engine.walkers.DataSource; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java index e068ff7ad..3e9e9db39 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java @@ -33,10 +33,10 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.engine.walkers.NanoSchedulable; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.TreeReducible; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java index 40471b50b..8161d4387 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java @@ -30,9 +30,9 @@ import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RefWalker; import org.broadinstitute.gatk.utils.collections.ExpandingArrayList; import org.broadinstitute.gatk.utils.collections.Pair; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java index 998448ecf..ccb714b45 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.tools.walkers.qc; import htsjdk.samtools.CigarOperator; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.report.GATKReport; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.report.GATKReport; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.engine.walkers.Requires; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java index 33d22cab1..6503766b6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java @@ -26,8 +26,8 @@ package org.broadinstitute.gatk.tools.walkers.qc; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.NanoSchedulable; import org.broadinstitute.gatk.engine.walkers.ReadWalker; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java index 90a131c2a..10094ac6a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java @@ -29,8 +29,8 @@ import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.engine.walkers.Requires; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java index b5a1e742d..9679baac3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java @@ -29,9 +29,9 @@ import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java index 6e872e3d4..7def2e0e3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java @@ -25,17 +25,16 @@ package org.broadinstitute.gatk.tools.walkers.qc; +import org.broadinstitute.gatk.engine.walkers.FailMethod; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.NanoSchedulable; import org.broadinstitute.gatk.engine.walkers.RefWalker; import org.broadinstitute.gatk.engine.walkers.TreeReducible; -import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; -import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; @@ -50,12 +49,6 @@ public class ErrorThrowing extends RefWalker implements TreeRed @Argument(fullName = "failMethod", shortName = "fail", doc = "Determines which method to fail in", required = false) public FailMethod failMethod = FailMethod.MAP; - public enum FailMethod { - MAP, - REDUCE, - TREE_REDUCE - } - // // Template code to allow us to build the walker, doesn't actually do anything // @@ -65,7 +58,7 @@ public class ErrorThrowing extends RefWalker implements TreeRed return null; if ( failMethod == FailMethod.MAP ) - fail(); + FailMethod.fail(exceptionToThrow); return 0; } @@ -78,33 +71,13 @@ public class ErrorThrowing extends RefWalker implements TreeRed @Override public Integer reduce(Integer value, Integer sum) { if ( value != null && failMethod == FailMethod.REDUCE ) - fail(); + FailMethod.fail(exceptionToThrow); return sum; } public Integer treeReduce(final Integer lhs, final Integer rhs) { if ( failMethod == FailMethod.TREE_REDUCE ) - fail(); + FailMethod.fail(exceptionToThrow); return rhs; } - - private void fail() { - if ( exceptionToThrow.equals("UserException") ) { - throw new UserException("UserException"); - } else if ( exceptionToThrow.equals("NullPointerException") ) { - throw new NullPointerException(); - } else if ( exceptionToThrow.equals("ReviewedGATKException") ) { - throw new ReviewedGATKException("ReviewedGATKException"); - } else if ( exceptionToThrow.equals("SamError1") ) { - throw new RuntimeException(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_1); - } else if ( exceptionToThrow.equals("SamError2") ) { - throw new RuntimeException(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_2); - } else if ( exceptionToThrow.equals("NoSpace1") ) { - throw new htsjdk.samtools.util.RuntimeIOException(new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)")); - } else if ( exceptionToThrow.equals("NoSpace2") ) { - throw new htsjdk.samtools.SAMException("Exception writing BAM index file", new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)")); - } else { - throw new UserException.BadArgumentValue("exception", "exception isn't a recognized value " + exceptionToThrow); - } - } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java index 83c2cc48b..7bd51249a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java @@ -27,8 +27,8 @@ package org.broadinstitute.gatk.tools.walkers.qc; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.NanoSchedulable; import org.broadinstitute.gatk.engine.walkers.ReadWalker; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java index 322cea6d9..8b59812bb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.tools.walkers.qc; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.LocusWalker; import org.broadinstitute.gatk.engine.walkers.NanoSchedulable; import org.broadinstitute.gatk.engine.walkers.TreeReducible; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java index 22ab7d1a7..ca9a76ab8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java @@ -30,9 +30,9 @@ import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java index ee8b68fbf..0b325e6a4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java @@ -29,9 +29,9 @@ import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.reference.ReferenceSequence; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RefWalker; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.exceptions.GATKException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java index 14a1de5f5..d6e2bbe0b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java @@ -31,8 +31,8 @@ import org.broadinstitute.gatk.utils.commandline.Advanced; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.engine.walkers.Requires; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java index 5f1d39693..4e4d131a2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java @@ -26,11 +26,11 @@ package org.broadinstitute.gatk.tools.walkers.qc; import org.broadinstitute.gatk.utils.commandline.*; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.Window; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java index de3c0dcec..1bbc3a2d6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java @@ -34,9 +34,9 @@ import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Hidden; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.engine.walkers.Requires; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java index f271fe900..008a14842 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java @@ -28,18 +28,19 @@ package org.broadinstitute.gatk.tools.walkers.readutils; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileWriter; import htsjdk.samtools.SAMReadGroupRecord; +import org.broadinstitute.gatk.engine.io.NWaySAMFileWriter; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Hidden; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; import org.broadinstitute.gatk.engine.iterators.ReadTransformersMode; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.baq.BAQ; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -181,7 +182,7 @@ public class PrintReads extends ReadWalker impleme if (!sampleNames.isEmpty()) samplesToChoose.addAll(sampleNames); - random = GenomeAnalysisEngine.getRandomGenerator(); + random = Utils.getRandomGenerator(); if (toolkit != null) { final SAMFileHeader outputHeader = toolkit.getSAMFileHeader().clone(); @@ -193,7 +194,7 @@ public class PrintReads extends ReadWalker impleme //Add the program record (if appropriate) and set up the writer final boolean preSorted = true; if (toolkit.getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) { - Utils.setupWriter(out, toolkit, outputHeader, preSorted, this, PROGRAM_RECORD_NAME); + NWaySAMFileWriter.setupWriter(out, toolkit, outputHeader, preSorted, this, PROGRAM_RECORD_NAME); } else { out.writeHeader(outputHeader); out.setPresorted(preSorted); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java index 6f0ee85ff..7e05a10c4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java @@ -38,8 +38,8 @@ import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Hidden; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java index f4ee4a499..3ef03c3d6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java @@ -30,10 +30,11 @@ import htsjdk.samtools.SAMFileWriter; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; +import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.DataSource; import org.broadinstitute.gatk.engine.walkers.ReadWalker; import org.broadinstitute.gatk.engine.walkers.Requires; @@ -41,7 +42,6 @@ import org.broadinstitute.gatk.engine.walkers.WalkerName; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.ReadUtils; import java.util.ArrayList; import java.util.HashMap; @@ -109,7 +109,7 @@ public class SplitSamFile extends ReadWalker implements TreeRedu public final Map> createIntervalTreeByContig(final IntervalBinding intervals) { final Map> byContig = new HashMap>(); - final List locs = intervals.getIntervals(getToolkit()); + final List locs = intervals.getIntervals(getToolkit().getGenomeLocParser()); // set up the map from contig -> interval tree for ( final String contig : getContigNames() ) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java index 7244a9417..281d8d346 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier; import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java index 7ebf96e7c..1732b6d8d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import htsjdk.variant.variantcontext.Allele; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java index 89b37f0f2..3ef087e51 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java index 8e202a74a..b0d1bbeee 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Molten; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java index 484541e88..6d2982c1c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java @@ -26,9 +26,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import org.broadinstitute.gatk.utils.Utils; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index c01aae1cc..7adcc05c8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -25,14 +25,14 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.samples.Sample; import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; -import org.broadinstitute.gatk.utils.MendelianViolation; +import org.broadinstitute.gatk.engine.samples.MendelianViolation; import htsjdk.variant.variantcontext.VariantContext; import java.util.Map; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java index 88543b505..e52923db6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java @@ -26,9 +26,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import org.broadinstitute.gatk.utils.Utils; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java index 0d3d4cf27..8beda5c56 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index 60a488117..c972d9a91 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import htsjdk.variant.variantcontext.Allele; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index 1919c5f5e..c5fa247ec 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import org.broadinstitute.gatk.utils.BaseUtils; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java index 664e5f245..337056fb0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import htsjdk.variant.vcf.VCFConstants; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java index 0984a2e73..a1c5b21f3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java index 91473306a..3309b815c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java @@ -27,9 +27,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; import htsjdk.samtools.util.IntervalTree; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval; import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; @@ -164,7 +164,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval { if ( walker.knownCNVsFile != null ) { knownCNVs = walker.createIntervalTreeByContig(walker.knownCNVsFile); - final List locs = walker.knownCNVsFile.getIntervals(walker.getToolkit()); + final List locs = walker.knownCNVsFile.getIntervals(walker.getToolkit().getGenomeLocParser()); logger.info(String.format("Creating known CNV list %s containing %d intervals covering %d bp", walker.knownCNVsFile.getSource(), locs.size(), IntervalUtils.intervalSize(locs))); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java index 1f7ed14fc..d7173d921 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary; import htsjdk.variant.vcf.VCFConstants; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java index 349979ada..b0108aa58 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java index f131ca751..72bfa4b8c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java @@ -26,8 +26,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; import org.broadinstitute.gatk.utils.commandline.RodBinding; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.Collections; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java index f90e7c5bc..cb64651ef 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java index 97e5e7222..72ea18718 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java index 03cba8cfc..2cf50e38f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java index 8fdd00726..1f01fc611 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java @@ -26,8 +26,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; import org.broadinstitute.gatk.utils.commandline.RodBinding; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java index c37f0031c..1ee8d0294 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java index 08ff9d4f5..abb517a01 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java index e5cb24077..6efc332a8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.Collections; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java index 8ee4e79b2..5b6a3e078 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java @@ -27,8 +27,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; import htsjdk.samtools.util.IntervalTree; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.interval.IntervalUtils; @@ -62,7 +62,7 @@ public class IntervalStratification extends VariantStratifier { if ( getVariantEvalWalker().intervalsFile == null ) throw new UserException.MissingArgument("stratIntervals", "Must be provided when IntervalStratification is enabled"); - final List locs = getVariantEvalWalker().intervalsFile.getIntervals(getVariantEvalWalker().getToolkit()); + final List locs = getVariantEvalWalker().intervalsFile.getIntervals(getVariantEvalWalker().getToolkit().getGenomeLocParser()); if ( locs.isEmpty() ) throw new UserException.BadArgumentValue("stratIntervals", "Contains no intervals. Perhaps the file is malformed or empty?"); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java index 00fec2a81..746e4967d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.util.SortableJexlVCMatchExp; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextUtils; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java index 0114bf24d..349535dc8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java @@ -26,8 +26,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; import org.broadinstitute.gatk.utils.commandline.RodBinding; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java index 7ad45e040..9884952fa 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java index bd0b6f1e2..90a6ece92 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java index c2ddd803f..549738ad7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff; import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.EffectType; import org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.InfoFieldKey; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java index 6eba4b450..493f4fe36 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java index 0832ebd13..a7a0543ce 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.Stratifier; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java index 0ba5b6077..46a9ab97b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import htsjdk.variant.variantcontext.VariantContext; import java.util.Collections; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java index 7e9f2da36..e8b7fe2ec 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java @@ -25,9 +25,9 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.util; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java index 6f623d48b..53b143b80 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java @@ -27,8 +27,8 @@ package org.broadinstitute.gatk.tools.walkers.varianteval.util; import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.commandline.RodBinding; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.StandardEval; import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java index aa69693b8..b6ca7a087 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java @@ -27,18 +27,18 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.TreeReducible; import org.broadinstitute.gatk.engine.walkers.Window; -import org.broadinstitute.gatk.tools.walkers.annotator.ChromosomeCountConstants; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.variant.ChromosomeCountConstants; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java index 73995bf93..6e8a9e7e9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java @@ -32,14 +32,14 @@ import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java index d2f251a42..e7a8cd23b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java @@ -27,16 +27,16 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFHeader; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java index 641047800..b80c1c4d9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java @@ -35,19 +35,19 @@ import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.Window; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.sam.AlignmentUtils; import htsjdk.variant.variantcontext.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java index 710aad576..4448226fc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java @@ -34,13 +34,13 @@ import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.writer.Options; import htsjdk.variant.vcf.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java index d50b4f20d..b14d2f5b3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java @@ -25,19 +25,19 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -134,7 +134,7 @@ public class RandomlySplitVariants extends RodWalker { final Collection vcs = tracker.getValues(variantCollection.variants, context.getLocation()); for ( final VariantContext vc : vcs ) { - final double random = GenomeAnalysisEngine.getRandomGenerator().nextDouble(); + final double random = Utils.getRandomGenerator().nextDouble(); if(splitToMany){ final int index = (int)(numOfFiles * random); writers[index].add(vc); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java index c9842c8bc..75f297c10 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java @@ -30,16 +30,16 @@ import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.TreeReducible; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.interval.IntervalMergingRule; import org.broadinstitute.gatk.utils.interval.IntervalSetRule; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java index db9d082b7..72dbcdf18 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java @@ -27,19 +27,18 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.TreeReducible; -import org.broadinstitute.gatk.tools.walkers.annotator.ChromosomeCountConstants; -import org.broadinstitute.gatk.utils.MendelianViolation; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.variant.ChromosomeCountConstants; +import org.broadinstitute.gatk.engine.samples.MendelianViolation; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -528,7 +527,7 @@ public class SelectVariants extends RodWalker implements TreeR } if ( !failedJexlMatch && !justRead && - ( !SELECT_RANDOM_FRACTION || GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom ) ) { + ( !SELECT_RANDOM_FRACTION || Utils.getRandomGenerator().nextDouble() < fractionRandom ) ) { vcfWriter.add(sub); } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java index 6b6e6ca82..6142bc08d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java @@ -31,9 +31,9 @@ import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.Window; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java index 9031bf7c1..c52c408a2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java @@ -31,13 +31,13 @@ import org.broadinstitute.gatk.engine.walkers.Window; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.QualityUtils; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java index 1f7b20ca3..b9954221f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java @@ -30,14 +30,14 @@ import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java index b51349afe..d7090235d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java @@ -30,15 +30,15 @@ import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.Window; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.QualityUtils; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import htsjdk.variant.vcf.VCFHeader; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java index 9a65a7062..62845501b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java @@ -27,18 +27,18 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFHeader; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java index 3e0e2ab5c..2e5b9a7b7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java @@ -30,22 +30,22 @@ import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.refdata.VariantContextAdaptors; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.refdata.VariantContextAdaptors; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; import org.broadinstitute.gatk.engine.walkers.Reference; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.engine.walkers.Window; import org.broadinstitute.gatk.tools.walkers.annotator.VariantOverlapAnnotator; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.codecs.hapmap.RawHapMapFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.*; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java index c622e24f1..108eb102f 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java @@ -23,15 +23,18 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.tools.walkers.diffengine; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Input; import org.broadinstitute.gatk.utils.commandline.Output; import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.diffengine.DiffElement; +import org.broadinstitute.gatk.utils.diffengine.DiffEngine; +import org.broadinstitute.gatk.utils.diffengine.Difference; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.help.HelpConstants; diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java index c3108f055..feefd5f60 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java @@ -1,55 +1,29 @@ /* -* By downloading the PROGRAM you agree to the following terms of use: +* Copyright (c) 2012 The Broad Institute * -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. * -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.tools.walkers.diffengine; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.broadinstitute.gatk.utils.BaseTest; diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java index 53b6d42d6..bb6d5bc1a 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java @@ -28,8 +28,8 @@ package org.broadinstitute.gatk.tools.walkers.readutils; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; -import org.broadinstitute.gatk.utils.sam.ArtificialReadsTraversal; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.engine.traversals.ArtificialReadsTraversal; import org.broadinstitute.gatk.utils.sam.ArtificialGATKSAMFileWriter; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java index 4a087025a..2928bba1e 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.utils.variant; +package org.broadinstitute.gatk.tools.walkers.variantutils; import htsjdk.tribble.AbstractFeatureReader; import htsjdk.tribble.Tribble; @@ -38,6 +38,7 @@ import htsjdk.tribble.util.TabixUtils; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import htsjdk.variant.vcf.VCFCodec; +import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; import org.testng.Assert; import org.testng.TestException; import org.testng.annotations.DataProvider; diff --git a/public/gatk-utils/pom.xml b/public/gatk-utils/pom.xml index 27660dd61..e1aae406a 100644 --- a/public/gatk-utils/pom.xml +++ b/public/gatk-utils/pom.xml @@ -25,10 +25,6 @@ samtools htsjdk - - picard - picard - log4j log4j @@ -41,26 +37,19 @@ it.unimi.dsi fastutil - - org.simpleframework - simple-xml - org.reflections reflections + org.slf4j - slf4j-log4j12 + slf4j-api org.freemarker freemarker - - org.apache.commons - commons-jexl - commons-lang commons-lang @@ -81,10 +70,6 @@ net.java.dev.jna jna - - net.java.dev.jets3t - jets3t - us.levk drmaa-gridengine @@ -117,6 +102,16 @@ + + org.apache.maven.plugins + maven-assembly-plugin + + + example-resources + ${gatk.generate-resources.phase} + + + org.apache.maven.plugins maven-dependency-plugin @@ -152,8 +147,6 @@ - org.apache.maven.plugins maven-invoker-plugin diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java index 194db6829..ecb8bbde5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java @@ -26,7 +26,6 @@ package org.broadinstitute.gatk.utils; import htsjdk.samtools.util.StringUtil; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -596,7 +595,7 @@ public class BaseUtils { * or {@code fromIndex} greater than {@code toIndex}. */ public static void fillWithRandomBases(final byte[] dest, final int fromIndex, final int toIndex) { - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); if (dest == null) throw new IllegalArgumentException("the dest array cannot be null"); if (fromIndex > toIndex) @@ -620,7 +619,7 @@ public class BaseUtils { int randomBaseIndex = excludeBaseIndex; while (randomBaseIndex == excludeBaseIndex) { - randomBaseIndex = GenomeAnalysisEngine.getRandomGenerator().nextInt(4); + randomBaseIndex = Utils.getRandomGenerator().nextInt(4); } return randomBaseIndex; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java index 81a2bdc52..3c6b48cc3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.gatk.utils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.VariantContext; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java index a918c0a0e..61261f217 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java @@ -32,7 +32,6 @@ import com.google.java.contract.Requires; import org.apache.commons.math.MathException; import org.apache.commons.math.distribution.NormalDistribution; import org.apache.commons.math.distribution.NormalDistributionImpl; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.exceptions.GATKException; @@ -482,7 +481,7 @@ public class MannWhitneyU { double comp = Double.compare(left.first.doubleValue(),right.first.doubleValue()); if ( comp > 0 ) { return 1; } if ( comp < 0 ) { return -1; } - return GenomeAnalysisEngine.getRandomGenerator().nextBoolean() ? -1 : 1; + return Utils.getRandomGenerator().nextBoolean() ? -1 : 1; } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java index 01aa13354..614cb927e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java @@ -29,7 +29,6 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.commons.math.distribution.ExponentialDistribution; import org.apache.commons.math.distribution.ExponentialDistributionImpl; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.math.BigDecimal; @@ -109,7 +108,7 @@ public class MathUtils { * @return a random int >= min and <= max */ public static int randomIntegerInRange( final int min, final int max ) { - return GenomeAnalysisEngine.getRandomGenerator().nextInt(max - min + 1) + min; + return Utils.getRandomGenerator().nextInt(max - min + 1) + min; } /** @@ -1130,7 +1129,7 @@ public class MathUtils { ArrayList chosen_balls = new ArrayList(k); for (int i = 0; i < k; i++) { //Integer chosen_ball = balls[rand.nextInt(k)]; - chosen_balls.add(GenomeAnalysisEngine.getRandomGenerator().nextInt(n)); + chosen_balls.add(Utils.getRandomGenerator().nextInt(n)); //balls.remove(chosen_ball); } @@ -1151,7 +1150,7 @@ public class MathUtils { chosen_balls.add(i); } - Collections.shuffle(chosen_balls, GenomeAnalysisEngine.getRandomGenerator()); + Collections.shuffle(chosen_balls, Utils.getRandomGenerator()); //return (ArrayList) chosen_balls.subList(0, k); return new ArrayList(chosen_balls.subList(0, k)); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java index d869037f8..22c7127c2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java @@ -28,7 +28,6 @@ package org.broadinstitute.gatk.utils; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java index d664ef689..408fd9e9f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java @@ -27,12 +27,7 @@ package org.broadinstitute.gatk.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import htsjdk.samtools.SAMFileHeader; -import htsjdk.samtools.SAMProgramRecord; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; -import org.broadinstitute.gatk.utils.text.TextFormattingUtils; import java.lang.reflect.Array; import java.math.BigInteger; @@ -49,6 +44,15 @@ import java.util.*; * To change this template use File | Settings | File Templates. */ public class Utils { + /** + * Static random number generator and seed. + */ + private static final long GATK_RANDOM_SEED = 47382911L; + private static Random randomGenerator = new Random(GATK_RANDOM_SEED); + public static Random getRandomGenerator() { return randomGenerator; } + public static void resetRandomGenerator() { randomGenerator.setSeed(GATK_RANDOM_SEED); } + public static void resetRandomGenerator(long seed) { randomGenerator.setSeed(seed); } + /** our log, which we want to capture anything from this class */ private static Logger logger = Logger.getLogger(Utils.class); @@ -563,79 +567,6 @@ public class Utils { array[i] = value; } - /** - * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and sets - * up the writer with the header and presorted status. - * - * @param originalHeader original header - * @param programRecord the program record for this program - */ - public static SAMFileHeader setupWriter(final SAMFileHeader originalHeader, final SAMProgramRecord programRecord) { - final SAMFileHeader header = originalHeader.clone(); - final List oldRecords = header.getProgramRecords(); - final List newRecords = new ArrayList(oldRecords.size()+1); - for ( SAMProgramRecord record : oldRecords ) - if ( (programRecord != null && !record.getId().startsWith(programRecord.getId()))) - newRecords.add(record); - - if (programRecord != null) { - newRecords.add(programRecord); - header.setProgramRecords(newRecords); - } - return header; - } - - /** - * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and returns - * the new header to be added to the BAM writer. - * - * @param toolkit the engine - * @param walker the walker object (so we can extract the command line) - * @param PROGRAM_RECORD_NAME the name for the PG tag - * @return a pre-filled header for the bam writer - */ - public static SAMFileHeader setupWriter(final GenomeAnalysisEngine toolkit, final SAMFileHeader originalHeader, final Object walker, final String PROGRAM_RECORD_NAME) { - final SAMProgramRecord programRecord = createProgramRecord(toolkit, walker, PROGRAM_RECORD_NAME); - return setupWriter(originalHeader, programRecord); - } - - /** - * Creates a program record for the program, adds it to the list of program records (@PG tags) in the bam file and sets - * up the writer with the header and presorted status. - * - * @param writer BAM file writer - * @param toolkit the engine - * @param preSorted whether or not the writer can assume reads are going to be added are already sorted - * @param walker the walker object (so we can extract the command line) - * @param PROGRAM_RECORD_NAME the name for the PG tag - */ - public static void setupWriter(GATKSAMFileWriter writer, GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean preSorted, Object walker, String PROGRAM_RECORD_NAME) { - SAMFileHeader header = setupWriter(toolkit, originalHeader, walker, PROGRAM_RECORD_NAME); - writer.writeHeader(header); - writer.setPresorted(preSorted); - } - - - /** - * Creates a program record (@PG) tag - * - * @param toolkit the engine - * @param walker the walker object (so we can extract the command line) - * @param PROGRAM_RECORD_NAME the name for the PG tag - * @return a program record for the tool - */ - public static SAMProgramRecord createProgramRecord(GenomeAnalysisEngine toolkit, Object walker, String PROGRAM_RECORD_NAME) { - final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME); - final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); - try { - final String version = headerInfo.getString("org.broadinstitute.gatk.tools.version"); - programRecord.setProgramVersion(version); - } catch (MissingResourceException e) { - // couldn't care less if the resource is missing... - } - programRecord.setCommandLine(toolkit.createApproximateCommandLineArgumentString(toolkit, walker)); - return programRecord; - } /** * Returns the number of combinations represented by this collection diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java index ccd4fdc44..0dfce0e99 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.arguments; +package org.broadinstitute.gatk.utils; import org.broadinstitute.gatk.utils.commandline.EnumerationArgumentDefault; @@ -32,7 +32,6 @@ import java.util.List; public class ValidationExclusion { - // our validation options public enum TYPE { @@ -64,4 +63,9 @@ public class ValidationExclusion { public boolean contains(TYPE t) { return (exclusions.contains(TYPE.ALL) || exclusions.contains(t)); } + + public static boolean lenientVCFProcessing(final TYPE val) { + return val == TYPE.ALL + || val == TYPE.LENIENT_VCF_PROCESSING; + } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java index 7313e19e6..4b69968e3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java @@ -27,8 +27,6 @@ package org.broadinstitute.gatk.utils.classloader; import org.apache.log4j.Level; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.WalkerManager; -import org.broadinstitute.gatk.engine.filters.FilterManager; import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -279,13 +277,7 @@ public class PluginManager { Class plugin = pluginsByName.get(pluginName); if( plugin == null ) { String errorMessage = formatErrorMessage(pluginCategory,pluginName); - if ( this.getClass().isAssignableFrom(FilterManager.class) ) { - throw new UserException.MalformedReadFilterException(errorMessage); - } else if ( this.getClass().isAssignableFrom(WalkerManager.class) ) { - throw new UserException.MalformedWalkerArgumentsException(errorMessage); - } else { - throw new UserException.CommandLineException(errorMessage); - } + throw createMalformedArgumentException(errorMessage); } try { return plugin.newInstance(); @@ -352,4 +344,13 @@ public class PluginManager { protected String formatErrorMessage(String pluginCategory, String pluginName ) { return String.format("Could not find %s with name: %s", pluginCategory,pluginName); } + + /** + * Creates a UserException with the appropriate message for this instance. + * @param errorMessage formatted error message from formatErrorMessage(). + * @return A UserException with the error message. + */ + protected UserException createMalformedArgumentException(final String errorMessage) { + throw new UserException.CommandLineException(errorMessage); + } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java index 915900388..a8ac99def 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java @@ -53,7 +53,7 @@ package org.broadinstitute.gatk.utils.codecs.beagle; import htsjdk.tribble.AsciiFeatureCodec; import htsjdk.tribble.exception.CodecLineParsingException; import htsjdk.tribble.readers.LineIterator; -import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec; +import org.broadinstitute.gatk.utils.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java index 9d60076ca..379fba036 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java @@ -29,7 +29,7 @@ import htsjdk.tribble.AsciiFeatureCodec; import htsjdk.tribble.Feature; import htsjdk.tribble.TribbleException; import htsjdk.tribble.readers.LineIterator; -import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec; +import org.broadinstitute.gatk.utils.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.Utils; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java index 226a35307..97ff961d9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java @@ -26,8 +26,8 @@ package org.broadinstitute.gatk.utils.codecs.refseq; import htsjdk.tribble.Feature; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java index 9a0115f66..cf6cefeb8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java @@ -25,8 +25,7 @@ package org.broadinstitute.gatk.utils.codecs.table; -import htsjdk.tribble.Feature; -import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec; +import org.broadinstitute.gatk.utils.refdata.ReferenceDependentFeatureCodec; import java.util.Arrays; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java index 1058d3e90..09af2f7a5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java @@ -27,7 +27,7 @@ package org.broadinstitute.gatk.utils.codecs.table; import htsjdk.tribble.AsciiFeatureCodec; import htsjdk.tribble.readers.LineIterator; -import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec; +import org.broadinstitute.gatk.utils.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java index 7af62bd9e..e5c7fad4e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.gatk.utils.collections; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java index 885e02d66..e372b4e02 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java @@ -25,8 +25,6 @@ package org.broadinstitute.gatk.utils.commandline; -import org.broadinstitute.gatk.engine.walkers.Multiplexer; - import java.util.*; /** diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java index 2d81cfcaa..e58d8888f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java @@ -25,8 +25,6 @@ package org.broadinstitute.gatk.utils.commandline; -import org.broadinstitute.gatk.engine.walkers.Multiplexer; - import java.util.*; /** * Represents a list of potential matches between the arguments defined diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java index 5bfc5166b..a1052261e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java @@ -25,11 +25,10 @@ package org.broadinstitute.gatk.utils.commandline; +import htsjdk.tribble.AbstractFeatureReader; import org.apache.log4j.Logger; import htsjdk.tribble.Feature; -import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager; -import org.broadinstitute.gatk.engine.walkers.Multiplex; -import org.broadinstitute.gatk.engine.walkers.Multiplexer; +import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager; import org.broadinstitute.gatk.utils.classloader.JVMUtils; import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; @@ -71,6 +70,15 @@ public abstract class ArgumentTypeDescriptor { throw new ReviewedGATKException("Can't process command-line arguments of type: " + type.getName()); } + /** + * Returns true if the file will be compressed. + * @param writerFileName Name of the file + * @return true if the file will be compressed. + */ + public static boolean isCompressed(String writerFileName) { + return writerFileName != null && AbstractFeatureReader.hasBlockCompressedExtension(writerFileName); + } + /** * Does this descriptor support classes of the given type? * @param type The type to check. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java index 80ebe2c23..0c3cbecc7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java @@ -29,11 +29,11 @@ import org.apache.log4j.FileAppender; import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.apache.log4j.PatternLayout; -import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.help.ApplicationDetails; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.help.HelpFormatter; +import org.broadinstitute.gatk.utils.text.TextFormattingUtils; import java.io.IOException; import java.util.*; @@ -295,6 +295,17 @@ public abstract class CommandLineProgram { Logger.getRootLogger().setLevel(par); } + public static String getVersionNumber() { + // TODO: Confirm that version is available elsewhere not on tools. + ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); + return headerInfo.containsKey("org.broadinstitute.gatk.utils.version") ? headerInfo.getString("org.broadinstitute.gatk.utils.version") : ""; + } + + public static String getBuildTime() { + ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("GATKText"); + return headerInfo.containsKey("build.timestamp") ? headerInfo.getString("build.timestamp") : ""; + } + /** * a function used to indicate an error occurred in the command line tool */ @@ -341,7 +352,7 @@ public abstract class CommandLineProgram { * Print help and exit. */ private static void printVersionAndExit() { - System.out.println(CommandLineGATK.getVersionNumber().toString()); + System.out.println(getVersionNumber().toString()); System.exit(0); } @@ -371,7 +382,7 @@ public abstract class CommandLineProgram { t.printStackTrace(); errorPrintf("------------------------------------------------------------------------------------------%n"); - errorPrintf("A GATK RUNTIME ERROR has occurred (version %s):%n", CommandLineGATK.getVersionNumber()); + errorPrintf("A GATK RUNTIME ERROR has occurred (version %s):%n", getVersionNumber()); errorPrintf("%n"); errorPrintf("This might be a bug. Please check the documentation guide to see if this is a known problem.%n"); errorPrintf("If not, please post the error message, with stack trace, to the GATK forum.%n"); @@ -389,7 +400,7 @@ public abstract class CommandLineProgram { throw new ReviewedGATKException("UserException found with no message!", e); errorPrintf("------------------------------------------------------------------------------------------%n"); - errorPrintf("A USER ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber()); + errorPrintf("A USER ERROR has occurred (version %s): %n", getVersionNumber()); errorPrintf("%n"); errorPrintf("This means that one or more arguments or inputs in your command are incorrect.%n"); errorPrintf("The error message below tells you what is the problem.%n"); @@ -411,7 +422,7 @@ public abstract class CommandLineProgram { throw new ReviewedGATKException("SamException found with no message!", t); errorPrintf("------------------------------------------------------------------------------------------%n"); - errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber()); + errorPrintf("A BAM ERROR has occurred (version %s): %n", getVersionNumber()); errorPrintf("%n"); errorPrintf("This means that there is something wrong with the BAM file(s) you provided.%n"); errorPrintf("The error message below tells you what is the problem.%n"); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java index 59048a93b..815b02d6b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java @@ -30,9 +30,8 @@ import htsjdk.tribble.AbstractFeatureReader; import htsjdk.tribble.Feature; import htsjdk.tribble.FeatureCodec; import htsjdk.tribble.FeatureReader; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec; -import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager; +import org.broadinstitute.gatk.utils.refdata.ReferenceDependentFeatureCodec; +import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -69,10 +68,6 @@ public final class IntervalBinding { return ( featureIntervals != null ? featureIntervals.getSource() : stringIntervals ); } - public List getIntervals(final GenomeAnalysisEngine toolkit) { - return getIntervals(toolkit.getGenomeLocParser()); - } - public List getIntervals(final GenomeLocParser genomeLocParser) { List intervals; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java index e771d1ed8..d00206b90 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers; +package org.broadinstitute.gatk.utils.commandline; import java.lang.annotation.*; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java index 969e288a5..3a6fb2f71 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers; +package org.broadinstitute.gatk.utils.commandline; import java.util.Collection; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java index 6ac204865..bbbb61778 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.contexts; +package org.broadinstitute.gatk.utils.contexts; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.HasGenomeLocation; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java index afeb1e735..82e1b0eb0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.contexts; +package org.broadinstitute.gatk.utils.contexts; import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.gatk.utils.GenomeLoc; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java index 201ea49fd..ae70402de 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.contexts; +package org.broadinstitute.gatk.utils.contexts; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java index 2c8cc7ae1..29a08cc9e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java index ebed91470..0e0b79741 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java index d10cfea8a..4960e6bfa 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.classloader.PluginManager; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java index dde9ca50d..651af07ba 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; import com.google.java.contract.Requires; import org.broadinstitute.gatk.utils.Utils; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java index acec38356..c84842dab 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; /** * Created by IntelliJ IDEA. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java index 903a073e0..43d947329 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java index c8794a703..25ebc032e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; public class Difference implements Comparable { final String path; // X.Y.Z diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java index 4a78448b6..9dc5e2e5e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java @@ -23,11 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; -import org.broadinstitute.gatk.engine.report.GATKReport; -import org.broadinstitute.gatk.engine.report.GATKReportColumn; -import org.broadinstitute.gatk.engine.report.GATKReportTable; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportColumn; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import java.io.File; import java.io.FileReader; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java index 23b213e91..a60209ad3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.walkers.diffengine; +package org.broadinstitute.gatk.utils.diffengine; import org.apache.log4j.Logger; import htsjdk.tribble.AbstractFeatureReader; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java index 0bcf4ee62..fd81e4ba7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.BaseUtils; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java index 715ef6eed..52ece95c1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; /** * Type of downsampling method to invoke. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java index 8ab0198b1..cdaec016c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import java.util.Collection; import java.util.List; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java index 94a3cc74b..5cb32386d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java @@ -23,11 +23,8 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; -import org.broadinstitute.gatk.engine.walkers.ActiveRegionWalker; -import org.broadinstitute.gatk.engine.walkers.LocusWalker; -import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.utils.exceptions.UserException; /** @@ -102,24 +99,6 @@ public class DownsamplingMethod { } } - public void checkCompatibilityWithWalker( Walker walker ) { - boolean isLocusTraversal = walker instanceof LocusWalker || walker instanceof ActiveRegionWalker; - - if ( isLocusTraversal && type == DownsampleType.ALL_READS && toCoverage != null ) { - throw new UserException("Downsampling to coverage with the ALL_READS method for locus-based traversals (eg., LocusWalkers) is not currently supported (though it is supported for ReadWalkers)."); - } - - // For locus traversals, ensure that the dcov value (if present) is not problematically low - if ( isLocusTraversal && type != DownsampleType.NONE && toCoverage != null && - toCoverage < MINIMUM_SAFE_COVERAGE_TARGET_FOR_LOCUS_BASED_TRAVERSALS ) { - throw new UserException(String.format("Locus-based traversals (ie., Locus and ActiveRegion walkers) require " + - "a minimum -dcov value of %d when downsampling to coverage. Values less " + - "than this can produce problematic downsampling artifacts while providing " + - "only insignificant improvements in memory usage in most cases.", - MINIMUM_SAFE_COVERAGE_TARGET_FOR_LOCUS_BASED_TRAVERSALS)); - } - } - public String toString() { StringBuilder builder = new StringBuilder("Downsampling Settings: "); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java index 6b398aba2..d7106b76a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import java.util.Collection; import java.util.Iterator; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java index bd236c0bc..9bfc13a13 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.sam.ReadUtils; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java index a2d613c5f..11d28c7d6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.ArrayList; @@ -66,7 +66,7 @@ public class FractionalDownsampler extends ReadsDownsampler @Override public void submit( final T newRead ) { - if ( GenomeAnalysisEngine.getRandomGenerator().nextInt(10000) < cutoffForInclusion || doNotDiscardItem(newRead) ) { + if ( Utils.getRandomGenerator().nextInt(10000) < cutoffForInclusion || doNotDiscardItem(newRead) ) { selectedReads.add(newRead); } else { diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java index 4ddf8dd87..c2113c4a3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java index 4ae7bc581..537a9f8c0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import org.broadinstitute.gatk.utils.MathUtils; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java index a5fdf24a9..313a432d3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java index 118bbbbeb..f289960ee 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java @@ -23,12 +23,12 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMRecordComparator; import htsjdk.samtools.SAMRecordCoordinateComparator; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import java.util.*; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java index 9263920f9..ed6b4394a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java index 9ef847e67..7cae97be5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java index 99a0bbd7a..e4a6ee464 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.*; @@ -137,7 +137,7 @@ public class ReservoirDownsampler extends ReadsDownsampler< isLinkedList = false; } - final int randomSlot = GenomeAnalysisEngine.getRandomGenerator().nextInt(totalDiscardableReadsSeen); + final int randomSlot = Utils.getRandomGenerator().nextInt(totalDiscardableReadsSeen); if ( randomSlot < targetSampleSize ) { reservoir.set(randomSlot, newRead); } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java index c825bae1f..2e6207410 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java index af0aa54c0..f150636f1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java index 3fc66cafe..cdbcf0f63 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.SAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java index 05f2ccfd7..b2f65585a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java @@ -25,7 +25,8 @@ package org.broadinstitute.gatk.utils.fasta; -import picard.PicardException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import htsjdk.samtools.SAMException; import htsjdk.samtools.reference.FastaSequenceIndex; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.reference.ReferenceSequence; @@ -171,6 +172,50 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { this(fasta, DEFAULT_CACHE_SIZE, preserveCase, false); } + /** + * Create reference data source from fasta file, after performing several preliminary checks on the file. + * This static utility was refactored from the constructor of ReferenceDataSource. + * Possibly may be better as an overloaded constructor. + * @param fastaFile Fasta file to be used as reference + * @return A new instance of a CachingIndexedFastaSequenceFile. + */ + public static CachingIndexedFastaSequenceFile checkAndCreate(final File fastaFile) { + // does the fasta file exist? check that first... + if (!fastaFile.exists()) + throw new UserException("The fasta file you specified (" + fastaFile.getAbsolutePath() + ") does not exist."); + + final boolean isGzipped = fastaFile.getAbsolutePath().endsWith(".gz"); + if ( isGzipped ) { + throw new UserException.CannotHandleGzippedRef(); + } + + final File indexFile = new File(fastaFile.getAbsolutePath() + ".fai"); + + // determine the name for the dict file + final String fastaExt = fastaFile.getAbsolutePath().endsWith("fa") ? "\\.fa$" : "\\.fasta$"; + final File dictFile = new File(fastaFile.getAbsolutePath().replaceAll(fastaExt, ".dict")); + + // It's an error if either the fai or dict file does not exist. The user is now responsible + // for creating these files. + if (!indexFile.exists()) { + throw new UserException.MissingReferenceFaiFile(indexFile, fastaFile); + } + if (!dictFile.exists()) { + throw new UserException.MissingReferenceDictFile(dictFile, fastaFile); + } + + // Read reference data by creating an IndexedFastaSequenceFile. + try { + return new CachingIndexedFastaSequenceFile(fastaFile); + } + catch (IllegalArgumentException e) { + throw new UserException.CouldNotReadInputFile(fastaFile, "Could not read reference sequence. The FASTA must have either a .fasta or .fa extension", e); + } + catch (Exception e) { + throw new UserException.CouldNotReadInputFile(fastaFile, e); + } + } + /** * Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened. * @@ -275,7 +320,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { SAMSequenceRecord contigInfo = super.getSequenceDictionary().getSequence(contig); if (stop > contigInfo.getSequenceLength()) - throw new PicardException("Query asks for data past end of contig"); + throw new SAMException("Query asks for data past end of contig"); if ( start < myCache.start || stop > myCache.stop || myCache.seq == null || myCache.seq.getContigIndex() != contigInfo.getSequenceIndex() ) { cacheMisses++; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java index 3b0adeda4..bf7b3ddc6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.tools.walkers.genotyper; +package org.broadinstitute.gatk.utils.genotyper; import htsjdk.variant.variantcontext.Allele; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java index 8d95fa43e..f5adb8a6e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.tools.walkers.genotyper; +package org.broadinstitute.gatk.utils.genotyper; import htsjdk.variant.variantcontext.Allele; import org.broadinstitute.gatk.utils.collections.Permutation; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java index 4f40f51ab..568535ade 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.tools.walkers.genotyper; +package org.broadinstitute.gatk.utils.genotyper; import htsjdk.variant.variantcontext.Allele; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java index 9238af7f6..d6530238b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.tools.walkers.genotyper; +package org.broadinstitute.gatk.utils.genotyper; import htsjdk.variant.variantcontext.Allele; import org.broadinstitute.gatk.utils.collections.IndexedSet; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java index 94022c827..7a92b4e24 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.tools.walkers.genotyper; +package org.broadinstitute.gatk.utils.genotyper; import org.broadinstitute.gatk.utils.collections.IndexedSet; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java index 1dd8a8a1f..56d12d026 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -27,7 +27,7 @@ package org.broadinstitute.gatk.utils.genotyper; import com.google.java.contract.Ensures; -import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.gatk.utils.downsampling.AlleleBiasedDownsamplingUtils; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.haplotype.Haplotype; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java index fa9fc300d..a792386e2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java @@ -29,8 +29,7 @@ import htsjdk.variant.variantcontext.Allele; import it.unimi.dsi.fastutil.ints.IntArrayList; import it.unimi.dsi.fastutil.objects.Object2IntMap; import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap; -import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils; -import org.broadinstitute.gatk.tools.walkers.genotyper.*; +import org.broadinstitute.gatk.utils.downsampling.AlleleBiasedDownsamplingUtils; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java index 29cb4287c..00d970824 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.tools.walkers.genotyper; +package org.broadinstitute.gatk.utils.genotyper; /** * A indexed set of samples. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java index 2071f5de0..8abfafb11 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.tools.walkers.genotyper; +package org.broadinstitute.gatk.utils.genotyper; import java.util.*; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java index e5eee12d2..271102d64 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java @@ -184,7 +184,7 @@ public class EventMap extends TreeMap { * Add VariantContext vc to this map, merging events with the same start sites if necessary * @param vc the variant context to add */ - protected void addVC(final VariantContext vc) { + public void addVC(final VariantContext vc) { addVC(vc, true); } @@ -193,7 +193,7 @@ public class EventMap extends TreeMap { * @param vc the variant context to add * @param merge should we attempt to merge it with an already existing element, or should we throw an error in that case? */ - protected void addVC(final VariantContext vc, final boolean merge) { + public void addVC(final VariantContext vc, final boolean merge) { if ( vc == null ) throw new IllegalArgumentException("vc cannot be null"); if ( containsKey(vc.getStart()) ) { diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java index 7b31b2a7b..153a9a4b4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java @@ -30,7 +30,7 @@ import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; import org.apache.commons.lang.ArrayUtils; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.sam.AlignmentUtils; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java index bd03add22..af56eb9b2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java @@ -41,8 +41,6 @@ import org.apache.commons.io.FileUtils; import org.apache.log4j.Level; import org.apache.log4j.Logger; import htsjdk.tribble.FeatureCodec; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.tools.walkers.qc.DocumentationTest; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.text.XReadLines; @@ -52,8 +50,7 @@ import java.util.*; /** * Javadoc Doclet that combines javadoc, GATK ParsingEngine annotations, and FreeMarker - * templates to produce PHP formatted GATKDocs for walkers - * and other classes. + * templates to produce PHP formatted GATKDocs for classes. *

* This document has the following workflow: *

@@ -71,7 +68,7 @@ import java.util.*; * The documented classes are restricted to only those with @DocumentedGATKFeature * annotation or are in the STATIC_DOCS class. */ -public class GATKDoclet { +public abstract class GATKDoclet { final protected static Logger logger = Logger.getLogger(GATKDoclet.class); /** @@ -98,13 +95,6 @@ public class GATKDoclet { protected static boolean testOnly = false; - /** - * Any class that's in this list will be included in the documentation - * when the -test argument is provided. Useful for debugging. - */ - private static final List> testOnlyKeepers = Arrays.asList( - DocumentationTest.class, CommandLineGATK.class, UserException.class); - /** * The javadoc root doc */ @@ -139,7 +129,7 @@ public class GATKDoclet { * @return Whether the JavaDoc run succeeded. * @throws java.io.IOException if output can't be written. */ - public static boolean start(RootDoc rootDoc) throws IOException { + protected boolean startProcessDocs(RootDoc rootDoc) throws IOException { logger.setLevel(Level.INFO); // load arguments @@ -166,7 +156,7 @@ public class GATKDoclet { throw new RuntimeException("-settings-dir " + settingsDir.getPath() + " is not a directory"); // process the docs - new GATKDoclet().processDocs(rootDoc); + processDocs(rootDoc); return true; } @@ -200,6 +190,15 @@ public class GATKDoclet { return showHiddenFeatures; } + /** + * Any class that's in this list will be included in the documentation + * when the -test argument is provided. Useful for debugging. + * Subclasses, such as WalkerDoclet, may add additional classes for debugging. + */ + protected List> getTestOnlyKeepers() { + return Collections.>singletonList(UserException.class); + } + /** * @param rootDoc */ @@ -292,12 +291,9 @@ public class GATKDoclet { Class clazz = getClassForClassDoc(doc); // don't add anything that's not DocumentationTest if we are in test mode - if (clazz != null && testOnly && !testOnlyKeepers.contains(clazz)) + if (clazz != null && testOnly && !getTestOnlyKeepers().contains(clazz)) continue; - //if ( clazz != null && clazz.getName().equals("org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalance")) - // logger.debug("foo"); - DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc); DocumentedGATKFeatureHandler handler = createHandler(doc, feature); if (handler != null && handler.includeInDocs(doc)) { @@ -324,7 +320,7 @@ public class GATKDoclet { private DocumentedGATKFeatureHandler createHandler(ClassDoc doc, DocumentedGATKFeatureObject feature) { if (feature != null) { if (feature.enable()) { - DocumentedGATKFeatureHandler handler = new GenericDocumentationHandler(); + DocumentedGATKFeatureHandler handler = createDocumentedGATKFeatureHandler(); handler.setDoclet(this); return handler; } else { @@ -335,6 +331,8 @@ public class GATKDoclet { return null; } + protected abstract DocumentedGATKFeatureHandler createDocumentedGATKFeatureHandler(); + /** * Returns the instantiated DocumentedGATKFeatureObject that describes the GATKDoc * structure we will apply to Doc. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java index fea149627..09c862aa0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java @@ -30,15 +30,10 @@ import com.google.java.contract.Requires; import com.sun.javadoc.ClassDoc; import com.sun.javadoc.FieldDoc; import com.sun.javadoc.Tag; -import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; import htsjdk.tribble.Feature; -import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.commandline.*; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.classloader.JVMUtils; import org.broadinstitute.gatk.utils.collections.Pair; @@ -46,14 +41,13 @@ import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.GATKException; import java.io.IOException; -import java.lang.annotation.Annotation; import java.lang.reflect.*; import java.util.*; /** * */ -public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { +public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { private static Logger logger = Logger.getLogger(GenericDocumentationHandler.class); /** @@ -155,7 +149,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * @param root */ protected void addArgumentBindings(Map root) { - ParsingEngine parsingEngine = createStandardGATKParsingEngine(); + ParsingEngine parsingEngine = createParsingEngine(); Map>> args = createArgumentMap(); root.put("arguments", args); @@ -361,289 +355,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * @param classToProcess the object to instantiate and query for the annotation * @param root the root of the document handler, to which we'll store collected annotations */ - private void getClazzAnnotations(Class classToProcess, Map root) { - // - // attempt to instantiate the class - final Object instance = makeInstanceIfPossible(classToProcess); - if (instance != null) { - final Class myClass = instance.getClass(); - // Get parallelism options - final HashSet> parallelOptions = getParallelism(myClass, new HashSet>()); - root.put("parallel", parallelOptions); - // Get annotation info (what type of annotation, standard etc.) - final HashSet annotInfo = getAnnotInfo(myClass, new HashSet()); - root.put("annotinfo", StringUtils.join(annotInfo, ", ")); - // Get annotation field (whether it goes in INFO or FORMAT) - root.put("annotfield", getAnnotField(myClass)); - // Get walker type if applicable - root.put("walkertype", getWalkerType(myClass)); - // Get partition type if applicable - root.put("partitiontype", getPartitionType(myClass)); - // Get read filter annotations (ReadFilters) if applicable - final HashSet> bucket= getReadFilters(myClass, new HashSet>()); - root.put("readfilters", bucket); - // Get default downsampling settings - final HashMap dsSettings = getDownSamplingSettings(myClass, new HashMap()); - root.put("downsampling", dsSettings); - // Get reference window size settings - final HashMap refwindow = getRefWindow(myClass, new HashMap()); - root.put("refwindow", refwindow); - // Get ActiveRegion size settings - final HashMap activeRegion = getActiveRegion(myClass, new HashMap()); - root.put("activeregion", activeRegion); - // Get annotation header line description if applicable - final Object annotDescriptLines = getAnnotDescript(instance, myClass); - root.put("annotdescript", annotDescriptLines); - - // anything else? - } else { - // put empty items to avoid blowups - root.put("parallel", new HashSet()); - root.put("annotinfo", ""); - root.put("annotfield", ""); - root.put("walkertype", ""); - root.put("partitiontype", ""); - root.put("readfilters", new HashSet>()); - root.put("downsampling", new HashMap()); - root.put("refwindow", new HashMap()); - root.put("activeregion", new HashMap()); - root.put("annotdescript", new ArrayList>()); - } - } - - /** - * Utility function that looks up annotation descriptions if applicable. - * - * @param myClass the class to query - * @return a hash map of descriptions, otherwise an empty map - */ - private Object getAnnotDescript(Object instance, Class myClass) { - // - // Check if the class has the method we want - for (Method classMethod : myClass.getMethods()) { - if (classMethod.toString().contains("getDescriptions") && classMethod.toString().contains("annotator")) { - try { - return classMethod.invoke(instance); - } catch (IllegalArgumentException e) { - } catch (IllegalAccessException e) { - } catch (InvocationTargetException e) { - } - } - } - return null; - } - - /** - * Utility function that checks which parallelism options are available for an instance of class c. - * - * @param myClass the class to query for the interfaces - * @param parallelOptions an empty HashSet in which to collect the info - * @return a hash set of parallelism options, otherwise an empty set - */ - private HashSet> getParallelism(Class myClass, HashSet> parallelOptions) { - // - // Retrieve interfaces - Class[] implementedInterfaces = myClass.getInterfaces(); - for (Class intfClass : implementedInterfaces) { - final HashMap nugget = new HashMap(); - if (intfClass.getSimpleName().equals("TreeReducible")) { - nugget.put("name", intfClass.getSimpleName()); - nugget.put("arg", HelpConstants.ARG_TREEREDUCIBLE); - nugget.put("link", HelpConstants.CMDLINE_GATK_URL + "#" + HelpConstants.ARG_TREEREDUCIBLE); - } else if (intfClass.getSimpleName().equals("NanoSchedulable")) { - nugget.put("name", intfClass.getSimpleName()); - nugget.put("arg", HelpConstants.ARG_NANOSCHEDULABLE); - nugget.put("link", HelpConstants.CMDLINE_GATK_URL + "#" + HelpConstants.ARG_NANOSCHEDULABLE); - } else { - continue; - } - parallelOptions.add(nugget); - } - // Look up superclasses recursively - final Class mySuperClass = myClass.getSuperclass(); - if (mySuperClass.getSimpleName().equals("Object")) { - return parallelOptions; - } - return getParallelism(mySuperClass, parallelOptions); - } - - /** - * Utility function that looks up whether the annotation goes in INFO or FORMAT field. - * - * @param myClass the class to query for the interfaces - * @return a String specifying the annotation field - */ - private final String getAnnotField(Class myClass) { - // - // Look up superclasses recursively until we find either - // GenotypeAnnotation or InfoFieldAnnotation - final Class mySuperClass = myClass.getSuperclass(); - if (mySuperClass == InfoFieldAnnotation.class) { - return "INFO (variant-level)"; - } else if (mySuperClass == GenotypeAnnotation.class) { - return "FORMAT (sample genotype-level)"; - } else if (mySuperClass.getSimpleName().equals("Object")) { - return ""; - } - return getAnnotField(mySuperClass); - } - - /** - * Utility function that determines the annotation type for an instance of class c. - * - * @param myClass the class to query for the interfaces - * @param annotInfo an empty HashSet in which to collect the info - * @return a hash set of the annotation types, otherwise an empty set - */ - private HashSet getAnnotInfo(Class myClass, HashSet annotInfo) { - // - // Retrieve interfaces - Class[] implementedInterfaces = myClass.getInterfaces(); - for (Class intfClass : implementedInterfaces) { - if (intfClass.getName().contains("Annotation")) { - annotInfo.add(intfClass.getSimpleName()); - } - } - // Look up superclasses recursively - final Class mySuperClass = myClass.getSuperclass(); - if (mySuperClass.getSimpleName().equals("Object")) { - return annotInfo; - } - return getAnnotInfo(mySuperClass, annotInfo); - } - - /** - * Utility function that determines the default downsampling settings for an instance of class c. - * - * @param myClass the class to query for the settings - * @param dsSettings an empty HashMap in which to collect the info - * @return a hash set of the downsampling settings, otherwise an empty set - */ - private HashMap getDownSamplingSettings(Class myClass, HashMap dsSettings) { - // - // Retrieve annotation - if (myClass.isAnnotationPresent(Downsample.class)) { - final Annotation thisAnnotation = myClass.getAnnotation(Downsample.class); - if(thisAnnotation instanceof Downsample) { - final Downsample dsAnnotation = (Downsample) thisAnnotation; - dsSettings.put("by", dsAnnotation.by().toString()); - dsSettings.put("to_cov", dsAnnotation.toCoverage()); - } - } - return dsSettings; - } - - /** - * Utility function that determines the reference window size for an instance of class c. - * - * @param myClass the class to query for the settings - * @param refWindow an empty HashMap in which to collect the info - * @return a HashMap of the window start and stop, otherwise an empty HashMap - */ - private HashMap getRefWindow(Class myClass, HashMap refWindow) { - // - // Retrieve annotation - if (myClass.isAnnotationPresent(Reference.class)) { - final Annotation thisAnnotation = myClass.getAnnotation(Reference.class); - if(thisAnnotation instanceof Reference) { - final Reference refAnnotation = (Reference) thisAnnotation; - refWindow.put("start", refAnnotation.window().start()); - refWindow.put("stop", refAnnotation.window().stop()); - } - } - return refWindow; - } - - /** - * Utility function that determines the ActiveRegion settings for an instance of class c. - * - * @param myClass the class to query for the settings - * @param activeRegion an empty HashMap in which to collect the info - * @return a HashMap of the ActiveRegion parameters, otherwise an empty HashMap - */ - private HashMap getActiveRegion(Class myClass, HashMap activeRegion) { - // - // Retrieve annotation - if (myClass.isAnnotationPresent(ActiveRegionTraversalParameters.class)) { - final Annotation thisAnnotation = myClass.getAnnotation(ActiveRegionTraversalParameters.class); - if(thisAnnotation instanceof ActiveRegionTraversalParameters) { - final ActiveRegionTraversalParameters arAnnotation = (ActiveRegionTraversalParameters) thisAnnotation; - activeRegion.put("ext", arAnnotation.extension()); - activeRegion.put("max", arAnnotation.maxRegion()); - activeRegion.put("min", arAnnotation.minRegion()); - } - } - return activeRegion; - } - - /** - * Utility function that determines the partition type of an instance of class c. - * - * @param myClass the class to query for the annotation - * @return the partition type if applicable, otherwise an empty string - */ - private String getPartitionType(Class myClass) { - // - // Retrieve annotation - if (myClass.isAnnotationPresent(PartitionBy.class)) { - final Annotation thisAnnotation = myClass.getAnnotation(PartitionBy.class); - if(thisAnnotation instanceof PartitionBy) { - final PartitionBy partAnnotation = (PartitionBy) thisAnnotation; - return partAnnotation.value().toString(); - } - } - return ""; - } - - /** - * Utility function that determines the type of walker subclassed by an instance of class c. - * - * @param myClass the class to query for the annotation - * @return the type of walker if applicable, otherwise an empty string - */ - private String getWalkerType(Class myClass) { - // - // Look up superclasses recursively until we find either Walker or Object - final Class mySuperClass = myClass.getSuperclass(); - if (mySuperClass.getSimpleName().equals("Walker")) { - return myClass.getSimpleName(); - } else if (mySuperClass.getSimpleName().equals("Object")) { - return ""; - } - return getWalkerType(mySuperClass); - } - - /** - * Utility function that finds the values of ReadFilters annotation applied to an instance of class c. - * - * @param myClass the class to query for the annotation - * @param bucket a container in which we store the annotations collected - * @return a hash set of values, otherwise an empty set - */ - private HashSet> getReadFilters(Class myClass, HashSet> bucket) { - // - // Retrieve annotation - if (myClass.isAnnotationPresent(ReadFilters.class)) { - final Annotation thisAnnotation = myClass.getAnnotation(ReadFilters.class); - if(thisAnnotation instanceof ReadFilters) { - final ReadFilters rfAnnotation = (ReadFilters) thisAnnotation; - for (Class filter : rfAnnotation.value()) { - // make hashmap of simplename and url - final HashMap nugget = new HashMap(); - nugget.put("name", filter.getSimpleName()); - nugget.put("filename", GATKDocUtils.phpFilenameForClass(filter)); - bucket.add(nugget); - } - } - } - // Look up superclasses recursively - final Class mySuperClass = myClass.getSuperclass(); - if (mySuperClass.getSimpleName().equals("Object")) { - return bucket; - } - return getReadFilters(mySuperClass, bucket); - } - + protected abstract void getClazzAnnotations(Class classToProcess, Map root); /** * Utility function that finds the value of fieldName in any fields of ArgumentCollection fields in @@ -725,7 +437,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * @param c * @return */ - private Object makeInstanceIfPossible(Class c) { + protected Object makeInstanceIfPossible(Class c) { Object instance = null; try { // don't try to make something where we will obviously fail @@ -755,8 +467,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * * @return */ - private ParsingEngine createStandardGATKParsingEngine() { - CommandLineProgram clp = new CommandLineGATK(); + private ParsingEngine createParsingEngine() { + CommandLineProgram clp = createCommandLineProgram(); try { CommandLineProgram.start(clp, new String[]{}, true); return clp.parser; @@ -765,6 +477,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { } } + protected abstract CommandLineProgram createCommandLineProgram(); + /** * Gets the javadocs associated with field name in classDoc. Throws a * runtime exception if this proves impossible. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java index 16257c6de..b72811c00 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java @@ -37,7 +37,6 @@ public class HelpConstants { */ public final static String ARG_TREEREDUCIBLE = "-nt"; public final static String ARG_NANOSCHEDULABLE = "-nct"; - public final static String CMDLINE_GATK_URL = GATK_DOCS_URL + "org_broadinstitute_gatk_engine_CommandLineGATK.php"; /** * Definition of the group names / categories of tools. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java index f28130b69..f225f4197 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java @@ -26,7 +26,6 @@ package org.broadinstitute.gatk.utils.help; import com.sun.javadoc.*; -import org.broadinstitute.gatk.engine.walkers.Walker; import org.broadinstitute.gatk.utils.Utils; import java.io.*; @@ -55,7 +54,7 @@ public class ResourceBundleExtractorDoclet { /** * Maintains a collection of classes that should really be documented. */ - protected final Set undocumentedWalkers = new HashSet(); + protected final Set undocumentedClasses = new HashSet(); protected String buildTimestamp = null, absoluteVersion = null; @@ -105,8 +104,8 @@ public class ResourceBundleExtractorDoclet { PackageDoc containingPackage = currentClass.containingPackage(); packages.add(containingPackage); - if(isRequiredJavadocMissing(currentClass) && isWalker(currentClass)) - undocumentedWalkers.add(currentClass.name()); + if(isRequiredJavadocMissing(currentClass) && shouldDocument(currentClass)) + undocumentedClasses.add(currentClass.name()); renderHelpText(DocletUtils.getClassName(currentClass),currentClass); } @@ -126,8 +125,8 @@ public class ResourceBundleExtractorDoclet { final String blink = "\u001B\u005B\u0035\u006D"; final String reset = "\u001B\u005B\u006D"; - if(undocumentedWalkers.size() > 0) - Utils.warnUser(String.format("The following walkers are currently undocumented: %s%s%s", blink, Utils.join(" ",undocumentedWalkers), reset)); + if(undocumentedClasses.size() > 0) + Utils.warnUser(String.format("The following are currently undocumented: %s%s%s", blink, Utils.join(" ", undocumentedClasses), reset)); } /** @@ -168,12 +167,25 @@ public class ResourceBundleExtractorDoclet { } /** - * Determine whether a given class is a walker. + * Determine whether a given class should be documented. * @param classDoc the type of the given class. - * @return True if the class of the given name is a walker. False otherwise. + * @return True if the class should be documented. False otherwise. */ - protected static boolean isWalker(ClassDoc classDoc) { - return DocletUtils.assignableToClass(classDoc, Walker.class, true); + protected static boolean shouldDocument(ClassDoc classDoc) { + // TODO: Code duplication with GATKDoclet, including DocletUtils.getClassForDoc(). + // TODO: Refactor common methods into DocletUtils, and possibly just use DocumentGATKFeatureObjects. + final Class docClass; + try { + docClass = (Class) DocletUtils.getClassForDoc(classDoc); + } catch (ClassNotFoundException e) { + return false; + } catch (NoClassDefFoundError e) { + return false; + } catch (UnsatisfiedLinkError e) { + return false; // naughty BWA bindings + } + final DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class); + return f != null && f.enable(); } /** diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java index 7fffb12e2..15a11023e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java @@ -27,6 +27,7 @@ package org.broadinstitute.gatk.utils.interval; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; +import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.util.Interval; import htsjdk.samtools.util.IntervalList; import htsjdk.samtools.SAMFileHeader; @@ -34,7 +35,6 @@ import org.apache.log4j.Logger; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.IntervalArgumentCollection; import org.broadinstitute.gatk.utils.commandline.IntervalBinding; -import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.GenomeLocSortedSet; @@ -42,6 +42,7 @@ import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.gatk.utils.text.XReadLines; import java.io.File; @@ -347,8 +348,8 @@ public class IntervalUtils { * @return A map of contig names with their sizes. */ public static Map getContigSizes(File reference) { - ReferenceDataSource referenceSource = new ReferenceDataSource(reference); - List locs = GenomeLocSortedSet.createSetFromSequenceDictionary(referenceSource.getReference().getSequenceDictionary()).toList(); + final ReferenceSequenceFile referenceSequenceFile = createReference(reference); + List locs = GenomeLocSortedSet.createSetFromSequenceDictionary(referenceSequenceFile.getSequenceDictionary()).toList(); Map lengths = new LinkedHashMap(); for (GenomeLoc loc: locs) lengths.put(loc.getContig(), loc.size()); @@ -583,13 +584,13 @@ public class IntervalUtils { * Setup the intervals to be processed */ public static GenomeLocSortedSet parseIntervalBindings( - final ReferenceDataSource referenceDataSource, + final ReferenceSequenceFile referenceSequenceFile, final List> intervals, final IntervalSetRule intervalSetRule, final IntervalMergingRule intervalMergingRule, final int intervalPadding, final List> excludeIntervals) { Pair includeExcludePair = parseIntervalBindingsPair( - referenceDataSource, intervals, intervalSetRule, intervalMergingRule, intervalPadding, excludeIntervals); + referenceSequenceFile, intervals, intervalSetRule, intervalMergingRule, intervalPadding, excludeIntervals); GenomeLocSortedSet includeSortedSet = includeExcludePair.getFirst(); GenomeLocSortedSet excludeSortedSet = includeExcludePair.getSecond(); @@ -601,7 +602,7 @@ public class IntervalUtils { } } - public static GenomeLocSortedSet parseIntervalArguments(final ReferenceDataSource referenceDataSource, IntervalArgumentCollection argCollection) { + public static GenomeLocSortedSet parseIntervalArguments(final ReferenceSequenceFile referenceSequenceFile, IntervalArgumentCollection argCollection) { GenomeLocSortedSet intervals = null; // return if no interval arguments at all @@ -613,7 +614,7 @@ public class IntervalUtils { // if include argument isn't given, create new set of all possible intervals final Pair includeExcludePair = IntervalUtils.parseIntervalBindingsPair( - referenceDataSource, + referenceSequenceFile, argCollection.intervals, argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding, argCollection.excludeIntervals); @@ -643,15 +644,15 @@ public class IntervalUtils { } public static Pair parseIntervalBindingsPair( - final ReferenceDataSource referenceDataSource, + final ReferenceSequenceFile referenceSequenceFile, final List> intervals, final IntervalSetRule intervalSetRule, final IntervalMergingRule intervalMergingRule, final int intervalPadding, final List> excludeIntervals) { - GenomeLocParser genomeLocParser = new GenomeLocParser(referenceDataSource.getReference()); + GenomeLocParser genomeLocParser = new GenomeLocParser(referenceSequenceFile); // if include argument isn't given, create new set of all possible intervals GenomeLocSortedSet includeSortedSet = ((intervals == null || intervals.size() == 0) ? - GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()) : + GenomeLocSortedSet.createSetFromSequenceDictionary(referenceSequenceFile.getSequenceDictionary()) : loadIntervals(intervals, intervalSetRule, intervalMergingRule, intervalPadding, genomeLocParser)); GenomeLocSortedSet excludeSortedSet = null; @@ -778,8 +779,8 @@ public class IntervalUtils { } public static void writeFlankingIntervals(File reference, File inputIntervals, File flankingIntervals, int basePairs) { - ReferenceDataSource referenceDataSource = new ReferenceDataSource(reference); - GenomeLocParser parser = new GenomeLocParser(referenceDataSource.getReference()); + final ReferenceSequenceFile referenceSequenceFile = createReference(reference); + GenomeLocParser parser = new GenomeLocParser(referenceSequenceFile); List originalList = intervalFileToList(parser, inputIntervals.getAbsolutePath()); if (originalList.isEmpty()) @@ -791,7 +792,7 @@ public class IntervalUtils { throw new UserException.MalformedFile(inputIntervals, "Unable to produce any flanks for the intervals"); SAMFileHeader samFileHeader = new SAMFileHeader(); - samFileHeader.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()); + samFileHeader.setSequenceDictionary(referenceSequenceFile.getSequenceDictionary()); IntervalList intervalList = new IntervalList(samFileHeader); int i = 0; for (GenomeLoc loc: flankingList) @@ -871,6 +872,10 @@ public class IntervalUtils { return sortAndMergeIntervals(parser, expanded, IntervalMergingRule.ALL).toList(); } + private static ReferenceSequenceFile createReference(final File fastaFile) { + return CachingIndexedFastaSequenceFile.checkAndCreate(fastaFile); + } + private static LinkedHashMap> splitByContig(List sorted) { LinkedHashMap> splits = new LinkedHashMap>(); GenomeLoc last = null; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java index 8ca5cfdbe..b91eb2526 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.iterators; +package org.broadinstitute.gatk.utils.iterators; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java index 0dc3e62a7..7507e0897 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.iterators; +package org.broadinstitute.gatk.utils.iterators; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; @@ -56,7 +56,7 @@ import java.util.Iterator; *

* This class adapts other SAMRecord iterators to the GATKSAMIterator */ -public class GATKSAMIteratorAdapter { +public class GATKSAMIteratorAdapter { public static GATKSAMIterator adapt(Iterator iter) { return new PrivateStringSAMIterator(iter); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java index 0bb545b6e..c4b867b55 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.iterators; +package org.broadinstitute.gatk.utils.iterators; import java.util.Iterator; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java index d9b158f85..d4c22a6ad 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java @@ -26,7 +26,6 @@ package org.broadinstitute.gatk.utils.locusiterator; import htsjdk.samtools.reference.IndexedFastaSequenceFile; -import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMRecordIterator; @@ -34,17 +33,13 @@ import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.CommandLineProgram; import org.broadinstitute.gatk.utils.commandline.Input; -import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.iterators.GATKSAMRecordIterator; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecordIterator; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.sam.GATKSamRecordFactory; import java.io.File; -import java.io.FileNotFoundException; import java.io.IOException; import java.util.*; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java index 72764e4df..ecbaaf670 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java @@ -26,7 +26,7 @@ package org.broadinstitute.gatk.utils.locusiterator; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import java.util.Iterator; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java index aaf61900e..4857ed595 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java @@ -32,13 +32,12 @@ import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.iterators.GATKSAMRecordIterator; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecordIterator; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.SampleUtils; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.utils.pileup.PileupElement; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; @@ -126,7 +125,9 @@ public final class LocusIteratorByState extends LocusIterator { * * @param samIterator the iterator of reads to process into pileups. Reads must be ordered * according to standard coordinate-sorted BAM conventions - * @param readInformation meta-information about how to process the reads (i.e., should we do downsampling?) + * @param downsamplingMethod information about how to downsample the reads + * @param includeReadsWithDeletionAtLoci Include reads with deletion at loci + * @param keepUniqueReadListInLIBS Keep unique read list in LIBS * @param genomeLocParser used to create genome locs * @param samples a complete list of samples present in the read groups for the reads coming from samIterator. * This is generally just the set of read group sample fields in the SAMFileHeader. This @@ -134,15 +135,17 @@ public final class LocusIteratorByState extends LocusIterator { * be mapped to this null sample */ public LocusIteratorByState(final Iterator samIterator, - final ReadProperties readInformation, + final DownsamplingMethod downsamplingMethod, + final boolean includeReadsWithDeletionAtLoci, + final boolean keepUniqueReadListInLIBS, final GenomeLocParser genomeLocParser, final Collection samples) { this(samIterator, - toDownsamplingInfo(readInformation), - readInformation.includeReadsWithDeletionAtLoci(), + toDownsamplingInfo(downsamplingMethod), + includeReadsWithDeletionAtLoci, genomeLocParser, samples, - readInformation.keepUniqueReadListInLIBS()); + keepUniqueReadListInLIBS); } /** @@ -160,7 +163,7 @@ public final class LocusIteratorByState extends LocusIterator { new LIBSDownsamplingInfo(false, 0), true, new GenomeLocParser(reader.getFileHeader().getSequenceDictionary()), - SampleUtils.getSAMFileSamples(reader.getFileHeader()), + ReadUtils.getSAMFileSamples(reader.getFileHeader()), false); } @@ -394,7 +397,7 @@ public final class LocusIteratorByState extends LocusIterator { } /** - * Create a LIBSDownsamplingInfo object from the requested info in ReadProperties + * Create a LIBSDownsamplingInfo object from the requested info in DownsamplingMethod * * LIBS will invoke the Reservoir and Leveling downsamplers on the read stream if we're * downsampling to coverage by sample. SAMDataSource will have refrained from applying @@ -403,16 +406,16 @@ public final class LocusIteratorByState extends LocusIterator { * split/re-assemble the read stream in SAMDataSource), and to enable partial downsampling * of reads (eg., using half of a read, and throwing the rest away). * - * @param readInfo GATK engine information about what should be done to the reads + * @param downsamplingMethod downsampling information about what should be done to the reads * @return a LIBS specific info holder about downsampling only */ - @Requires("readInfo != null") + @Requires("downsamplingMethod != null") @Ensures("result != null") - private static LIBSDownsamplingInfo toDownsamplingInfo(final ReadProperties readInfo) { - final boolean performDownsampling = readInfo.getDownsamplingMethod() != null && - readInfo.getDownsamplingMethod().type == DownsampleType.BY_SAMPLE && - readInfo.getDownsamplingMethod().toCoverage != null; - final int coverage = performDownsampling ? readInfo.getDownsamplingMethod().toCoverage : 0; + private static LIBSDownsamplingInfo toDownsamplingInfo(final DownsamplingMethod downsamplingMethod) { + final boolean performDownsampling = downsamplingMethod != null && + downsamplingMethod.type == DownsampleType.BY_SAMPLE && + downsamplingMethod.toCoverage != null; + final int coverage = performDownsampling ? downsamplingMethod.toCoverage : 0; return new LIBSDownsamplingInfo(performDownsampling, coverage); } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java index e6d49c354..8e16c1771 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java @@ -30,8 +30,8 @@ import com.google.java.contract.Invariant; import com.google.java.contract.Requires; import htsjdk.samtools.CigarOperator; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.downsampling.Downsampler; -import org.broadinstitute.gatk.engine.downsampling.LevelingDownsampler; +import org.broadinstitute.gatk.utils.downsampling.Downsampler; +import org.broadinstitute.gatk.utils.downsampling.LevelingDownsampler; import java.util.Iterator; import java.util.LinkedList; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java index 825cb350a..46a88588f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.utils.locusiterator; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.downsampling.Downsampler; -import org.broadinstitute.gatk.engine.downsampling.PassThroughDownsampler; -import org.broadinstitute.gatk.engine.downsampling.ReservoirDownsampler; +import org.broadinstitute.gatk.utils.downsampling.Downsampler; +import org.broadinstitute.gatk.utils.downsampling.PassThroughDownsampler; +import org.broadinstitute.gatk.utils.downsampling.ReservoirDownsampler; import java.util.*; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java index 6c4460cb3..b84afcfdc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java @@ -51,6 +51,8 @@ public abstract class PairHMM { protected byte[] previousHaplotypeBases; protected int hapStartIndex; + public static final byte BASE_QUALITY_SCORE_THRESHOLD = (byte) 18; // Base quals less than this value are squashed down to min possible qual + public enum HMM_IMPLEMENTATION { /* Very slow implementation which uses very accurate log10 sum functions. Only meant to be used as a reference test implementation */ EXACT, diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java index 29484048e..8728bb5de 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java @@ -46,7 +46,7 @@ public class PairHMMReadyHaplotypes implements Iterable positions = new TreeSet(); for (int i = 0; i < desiredCoverage; /* no update */) { - if (positions.add(GenomeAnalysisEngine.getRandomGenerator().nextInt(getNumberOfElements()))) + if (positions.add(Utils.getRandomGenerator().nextInt(getNumberOfElements()))) i++; } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java index 7296c39ae..79631a244 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata; +package org.broadinstitute.gatk.utils.refdata; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.HasGenomeLocation; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java index 7ccf6e572..f4fd40f7d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata; +package org.broadinstitute.gatk.utils.refdata; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.commandline.RodBinding; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java index 9bff00dd8..d8cbbd6be 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java @@ -23,9 +23,8 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata; +package org.broadinstitute.gatk.utils.refdata; -import htsjdk.tribble.FeatureCodec; import org.broadinstitute.gatk.utils.GenomeLocParser; /** diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java index 95de83208..daa0a3cbe 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata; +package org.broadinstitute.gatk.utils.refdata; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.HasGenomeLocation; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java index 4126214cf..9eb4b34e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java @@ -1,36 +1,36 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* Permission is hereby granted, free of charge, to any person -* obtaining a copy of this software and associated documentation -* files (the "Software"), to deal in the Software without -* restriction, including without limitation the rights to use, -* copy, modify, merge, publish, distribute, sublicense, and/or sell -* copies of the Software, and to permit persons to whom the -* Software is furnished to do so, subject to the following -* conditions: -* -* The above copyright notice and this permission notice shall be -* included in all copies or substantial portions of the Software. -* -* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR -* THE USE OR OTHER DEALINGS IN THE SOFTWARE. -*/ - -package org.broadinstitute.gatk.engine.refdata; +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.utils.refdata; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.util.CloseableIterator; -import org.broadinstitute.gatk.engine.iterators.PushbackIterator; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.iterators.PushbackIterator; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java index 82a826c10..d2c11407a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata; +package org.broadinstitute.gatk.utils.refdata; import htsjdk.samtools.util.SequenceUtil; import htsjdk.tribble.Feature; import htsjdk.tribble.annotation.Strand; import htsjdk.tribble.dbsnp.OldDbSNPFeature; import htsjdk.tribble.gelitext.GeliTextFeature; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.classloader.PluginManager; import org.broadinstitute.gatk.utils.codecs.hapmap.RawHapMapFeature; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java index e9e9714cb..bc444b784 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java @@ -23,4 +23,4 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata; \ No newline at end of file +package org.broadinstitute.gatk.utils.refdata; \ No newline at end of file diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java index d466f3f1e..d69a37476 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java @@ -23,15 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.tracks; +package org.broadinstitute.gatk.utils.refdata.tracks; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.tribble.Feature; import htsjdk.tribble.FeatureCodec; import htsjdk.tribble.NameAwareCodec; -import org.broadinstitute.gatk.engine.refdata.ReferenceDependentFeatureCodec; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.refdata.ReferenceDependentFeatureCodec; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.classloader.PluginManager; import htsjdk.variant.vcf.AbstractVCFCodec; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java index 5c18d3a8e..a0473c8a4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java @@ -23,14 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.tracks; +package org.broadinstitute.gatk.utils.refdata.tracks; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import htsjdk.tribble.index.Index; import htsjdk.tribble.index.MutableIndex; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; +import org.broadinstitute.gatk.utils.ValidationExclusion; import org.broadinstitute.gatk.utils.SequenceDictionaryUtils; import java.util.List; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java index 51cb8f443..ef8b27dcc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.tracks; +package org.broadinstitute.gatk.utils.refdata.tracks; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.util.CloseableIterator; @@ -32,8 +32,8 @@ import htsjdk.tribble.AbstractFeatureReader; import htsjdk.tribble.CloseableTribbleIterator; import htsjdk.tribble.Feature; import htsjdk.tribble.FeatureCodec; -import org.broadinstitute.gatk.engine.refdata.utils.FeatureToGATKFeatureIterator; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.FeatureToGATKFeatureIterator; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java index dc9e96728..86a561ade 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.tracks; +package org.broadinstitute.gatk.utils.refdata.tracks; import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; @@ -34,12 +34,11 @@ import htsjdk.tribble.TribbleException; import htsjdk.tribble.index.Index; import htsjdk.tribble.index.IndexFactory; import htsjdk.tribble.util.LittleEndianOutputStream; +import org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; -import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet.RMDStorageType; +import org.broadinstitute.gatk.utils.ValidationExclusion; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet.RMDStorageType; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; @@ -111,7 +110,7 @@ public class RMDTrackBuilder { // extends PluginManager { this.dict = dict; this.validationExclusionType = validationExclusionType; this.genomeLocParser = genomeLocParser; - this.featureManager = new FeatureManager(GenomeAnalysisEngine.lenientVCFProcessing(validationExclusionType)); + this.featureManager = new FeatureManager(ValidationExclusion.lenientVCFProcessing(validationExclusionType)); this.disableAutoIndexCreation = disableAutoIndexCreation; this.sampleRenameMap = sampleRenameMap; } @@ -142,7 +141,7 @@ public class RMDTrackBuilder { // extends PluginManager { // return a feature reader track Pair pair; - if (VCFWriterArgumentTypeDescriptor.isCompressed(inputFile.toString())) + if (ArgumentTypeDescriptor.isCompressed(inputFile.toString())) pair = createTabixIndexedFeatureSource(descriptor, name, inputFile); else pair = getFeatureSource(descriptor, name, inputFile, fileDescriptor.getStorageType()); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java index 6fb073e12..013a6c2ad 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.samtools.util.CloseableIterator; import htsjdk.tribble.CloseableTribbleIterator; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java index 8fc549c00..73ebf3cc8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.samtools.SAMSequenceDictionary; import org.broadinstitute.gatk.utils.GenomeLoc; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java index 4d08f1bca..e638ab48e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java @@ -23,10 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.tribble.Feature; -import org.broadinstitute.gatk.engine.refdata.ReferenceOrderedDatum; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.HasGenomeLocation; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java index 96c60b9d8..42fa9ffb1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.util.CloseableIterator; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java index 9fa3d1e11..3c79fc5fd 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import org.broadinstitute.gatk.utils.commandline.Tags; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java index b859edc10..025835275 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.HasGenomeLocation; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java index 660ea95c1..056581351 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.report; +package org.broadinstitute.gatk.utils.report; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java index ffdefff36..d672c1ba8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.report; +package org.broadinstitute.gatk.utils.report; import org.apache.commons.lang.math.NumberUtils; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java index 664b503b0..97c012a5a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.report; +package org.broadinstitute.gatk.utils.report; /** * Column width and left/right alignment. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java index acfa74f25..d522dff35 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.report; +package org.broadinstitute.gatk.utils.report; import java.util.EnumSet; import java.util.HashMap; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java index 5f7f7670c..359460bd0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.report; +package org.broadinstitute.gatk.utils.report; import org.broadinstitute.gatk.utils.commandline.Gatherer; import org.broadinstitute.gatk.utils.exceptions.UserException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java index 6a1e456d4..018d05500 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.report; +package org.broadinstitute.gatk.utils.report; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.text.TextFormattingUtils; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java index 226365b80..e87e107c0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java @@ -23,9 +23,8 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.report; +package org.broadinstitute.gatk.utils.report; -import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; public enum GATKReportVersion { diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java index 0821f4604..99fd76213 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java @@ -28,7 +28,6 @@ package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.ProgressLoggerInterface; -import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java index 84978c1ef..a468dc06b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java @@ -30,8 +30,8 @@ import htsjdk.samtools.SamFileHeaderMerger; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIteratorAdapter; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIteratorAdapter; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.util.*; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java index 8434e158d..e82355da9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java @@ -89,7 +89,7 @@ public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator { * @param header the associated header * @param pattern the pattern to implement */ - ArtificialPatternedSAMIterator( int startingChr, int endingChr, int readCount, int unmappedReadCount, SAMFileHeader header, PATTERN pattern ) { + public ArtificialPatternedSAMIterator( int startingChr, int endingChr, int readCount, int unmappedReadCount, SAMFileHeader header, PATTERN pattern ) { super(startingChr, endingChr, readCount, unmappedReadCount, header); mPattern = pattern; this.readCount = readCount; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java index b133e9c55..e4bdfbc23 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java @@ -27,7 +27,7 @@ package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import java.util.Iterator; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java index 7fb43efab..bad7ef643 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java @@ -26,7 +26,7 @@ package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.*; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java index 27e25d39c..93d27f7d5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java @@ -27,8 +27,8 @@ package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIteratorAdapter; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIteratorAdapter; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java index c60aae842..7949dd49e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.io; +package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileWriter; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java index 6d02acd4a..cc2b77895 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java @@ -23,10 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.iterators; +package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.util.CloseableIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import java.util.Iterator; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java index 7fc1b40f7..ce56a329f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java @@ -29,8 +29,6 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import htsjdk.samtools.*; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; @@ -57,6 +55,22 @@ public class ReadUtils { private static final int DEFAULT_ADAPTOR_SIZE = 100; public static final int CLIPPING_GOAL_NOT_REACHED = -1; + /** + * Pull out the samples from a SAMFileHeader; + * note that we use a TreeSet so that they are sorted + * + * @param header the sam file header + * @return list of strings representing the sample names + */ + public static Set getSAMFileSamples(final SAMFileHeader header) { + // get all of the unique sample names + final Set samples = new TreeSet(); + List readGroups = header.getReadGroups(); + for ( SAMReadGroupRecord readGroup : readGroups ) + samples.add(readGroup.getSample()); + return samples; + } + /** * A marker to tell which end of the read has been clipped */ @@ -130,27 +144,6 @@ public class ReadUtils { */ public enum ReadAndIntervalOverlap {NO_OVERLAP_CONTIG, NO_OVERLAP_LEFT, NO_OVERLAP_RIGHT, NO_OVERLAP_HARDCLIPPED_LEFT, NO_OVERLAP_HARDCLIPPED_RIGHT, OVERLAP_LEFT, OVERLAP_RIGHT, OVERLAP_LEFT_AND_RIGHT, OVERLAP_CONTAINED} - /** - * Creates a SAMFileWriter using all of the features currently set in the engine (command line arguments, ReadTransformers, etc) - * @param file the filename to write to - * @param engine the engine - * @return a SAMFileWriter with the correct options set - */ - public static SAMFileWriter createSAMFileWriter(final String file, final GenomeAnalysisEngine engine) { - final SAMFileWriterStub output = new SAMFileWriterStub(engine, new File(file)); - output.processArguments(engine.getArguments()); - return output; - } - - /** - * As {@link #createSAMFileWriter(String, org.broadinstitute.gatk.engine.GenomeAnalysisEngine)}, but also sets the header - */ - public static SAMFileWriter createSAMFileWriter(final String file, final GenomeAnalysisEngine engine, final SAMFileHeader header) { - final SAMFileWriterStub output = (SAMFileWriterStub) createSAMFileWriter(file, engine); - output.writeHeader(header); - return output; - } - /** * is this base inside the adaptor of the read? * @@ -757,7 +750,7 @@ public class ReadUtils { * @return an array with randomized base qualities between 0 and 50 */ public static byte[] createRandomReadQuals(int length) { - Random random = GenomeAnalysisEngine.getRandomGenerator(); + Random random = Utils.getRandomGenerator(); byte[] quals = new byte[length]; for (int i = 0; i < length; i++) quals[i] = (byte) random.nextInt(50); @@ -772,7 +765,7 @@ public class ReadUtils { * @return an array with randomized bases (A-N) with equal probability */ public static byte[] createRandomReadBases(int length, boolean allowNs) { - Random random = GenomeAnalysisEngine.getRandomGenerator(); + Random random = Utils.getRandomGenerator(); int numberOfBases = allowNs ? 5 : 4; byte[] bases = new byte[length]; for (int i = 0; i < length; i++) { diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java index ef5aaa040..4b93c3b7e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.datasources.reads; +package org.broadinstitute.gatk.utils.sam; import org.broadinstitute.gatk.utils.commandline.Tags; @@ -40,12 +40,12 @@ public class SAMReaderID implements Comparable { * The SAM file at the heart of this reader. SAMReaderID * currently supports only file-based readers. */ - protected final File samFile; + private final File samFile; /** * A list of tags associated with this BAM file. */ - protected final Tags tags; + private final Tags tags; /** * Creates an identifier for a SAM file based on read. @@ -79,6 +79,15 @@ public class SAMReaderID implements Comparable { return samFile.getAbsolutePath(); } + /** + * Gets the SAM file at the heart of this reader. SAMReaderID + * currently supports only file-based readers. + * @return the SAM file at the heart of this reader. + */ + public File getSamFile() { + return samFile; + } + /** * Gets the tags associated with the given BAM file. * @return A collection of the tags associated with this file. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java index d6e1bcbea..33a4b7d63 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java @@ -28,9 +28,9 @@ package org.broadinstitute.gatk.utils.text; import org.broadinstitute.gatk.utils.commandline.ParsingEngine; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; -import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager; -import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; +import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager; +import org.broadinstitute.gatk.utils.refdata.utils.RMDTriplet; import org.broadinstitute.gatk.utils.exceptions.UserException; import java.io.File; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java index 67fc0a406..72ed4e4f6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.tools.walkers.annotator; +package org.broadinstitute.gatk.utils.variant; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFInfoHeaderLine; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java index a099d8c9c..88f689b2d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java @@ -134,7 +134,7 @@ public class GATKVariantContextUtils { * @param loc if not null, ignore records that do not begin at this start location * @return possibly null Allele */ - protected static Allele determineReferenceAllele(final List VCs, final GenomeLoc loc) { + public static Allele determineReferenceAllele(final List VCs, final GenomeLoc loc) { Allele ref = null; for ( final VariantContext vc : VCs ) { diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java new file mode 100644 index 000000000..3263d9bf6 --- /dev/null +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java @@ -0,0 +1,92 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.utils.variant; + +import htsjdk.tribble.FeatureCodec; +import htsjdk.tribble.FeatureCodecHeader; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeader; +import org.broadinstitute.gatk.utils.collections.Pair; + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.util.Iterator; + +/* +* NOTE: Refactored out of GATKVCFUtils +*/ +public class VCIterable implements Iterable, Iterator { + final SOURCE source; + final FeatureCodec codec; + final VCFHeader header; + + VCIterable(final SOURCE source, final FeatureCodec codec, final VCFHeader header) { + this.source = source; + this.codec = codec; + this.header = header; + } + + /** + * Utility class to read all of the VC records from a file + * + * @param file + * @param codec + * @return + * @throws java.io.IOException + */ + public final static Pair> readAllVCs( final File file, final FeatureCodec codec) throws IOException { + // read in the features + SOURCE source = codec.makeSourceFromStream(new FileInputStream(file)); + FeatureCodecHeader header = codec.readHeader(source); + final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue(); + return new Pair<>(vcfHeader, new VCIterable<>(source, codec, vcfHeader)); + } + + @Override + public Iterator iterator() { + return this; + } + + @Override + public boolean hasNext() { + return ! codec.isDone(source); + } + + @Override + public VariantContext next() { + try { + final VariantContext vc = codec.decode(source); + return vc == null ? null : vc.fullyDecode(header, false); + } catch ( IOException e ) { + throw new RuntimeException(e); + } + } + + @Override + public void remove() { + } +} diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java index ca579223e..5689dbc4c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java @@ -41,12 +41,11 @@ import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.apache.log4j.PatternLayout; import org.apache.log4j.spi.LoggingEvent; +import org.broadinstitute.gatk.utils.variant.VCIterable; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.commandline.CommandLineUtils; -import org.broadinstitute.gatk.utils.crypt.CryptUtils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.io.IOUtils; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import org.testng.Assert; import org.testng.Reporter; import org.testng.SkipException; @@ -134,14 +133,12 @@ public abstract class BaseTest { public static final String privateTestDir = new File(gatkDirectory, privateTestDirRelative).getAbsolutePath() + "/"; protected static final String privateTestDirRoot = privateTestDir.replace(privateTestDirRelative, ""); - private static final String publicTestDirRelative = "public/gatk-engine/src/test/resources/"; + private static final String publicTestDirRelative = "public/gatk-utils/src/test/resources/"; public static final String publicTestDir = new File(gatkDirectory, publicTestDirRelative).getAbsolutePath() + "/"; protected static final String publicTestDirRoot = publicTestDir.replace(publicTestDirRelative, ""); public static final String keysDataLocation = validationDataLocation + "keys/"; - public static final String gatkKeyFile = CryptUtils.GATK_USER_KEY_DIRECTORY + "gsamembers_broadinstitute.org.key"; - public static final String exampleFASTA = publicTestDir + "exampleFASTA.fasta"; public final static String NA12878_PCRFREE = privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam"; @@ -491,8 +488,8 @@ public abstract class BaseTest { } public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile) throws IOException { - final Pair> vcfData = GATKVCFUtils.readAllVCs(vcfFile, new VCFCodec()); - final Pair> bcfData = GATKVCFUtils.readAllVCs(bcfFile, new BCF2Codec()); + final Pair> vcfData = VCIterable.readAllVCs(vcfFile, new VCFCodec()); + final Pair> bcfData = VCIterable.readAllVCs(bcfFile, new BCF2Codec()); assertVCFHeadersAreEqual(bcfData.getFirst(), vcfData.getFirst()); assertVariantContextStreamsAreEqual(bcfData.getSecond(), vcfData.getSecond()); } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java index b532bafa9..83dfc8cd2 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java @@ -25,8 +25,6 @@ package org.broadinstitute.gatk.utils; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -159,8 +157,8 @@ public class BaseUtilsUnitTest extends BaseTest { final Object[][] result = new Object[testCount][]; - GenomeAnalysisEngine.resetRandomGenerator(); - final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); + Utils.resetRandomGenerator(); + final Random rnd = Utils.getRandomGenerator(); for (int i = 0; i < testCount; i++) { final int size = (int) Math.max(0,rnd.nextDouble() * testSizeDeviation + testSizeAverage); diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java index 87a5914a3..5a0bc0bbf 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java @@ -25,7 +25,6 @@ package org.broadinstitute.gatk.utils; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -43,7 +42,7 @@ public class BitSetUtilsUnitTest { @BeforeClass public void init() { - random = GenomeAnalysisEngine.getRandomGenerator(); + random = Utils.getRandomGenerator(); } @Test(enabled = true) diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java index d7c992906..b753bc2fa 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java @@ -27,7 +27,7 @@ package org.broadinstitute.gatk.utils; import org.apache.commons.io.FileUtils; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.engine.walkers.diffengine.DiffEngine; +import org.broadinstitute.gatk.utils.diffengine.DiffEngine; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import java.io.*; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java index 6ccb0c976..c53c01bd5 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java @@ -28,8 +28,6 @@ package org.broadinstitute.gatk.utils; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java index a303f2c8b..dc3909e65 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java @@ -26,7 +26,6 @@ package org.broadinstitute.gatk.utils; import org.apache.commons.io.FileUtils; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.io.IOUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; @@ -189,7 +188,7 @@ public class UtilsUnitTest extends BaseTest { // good. } } else { - final Random rdn = GenomeAnalysisEngine.getRandomGenerator(); + final Random rdn = Utils.getRandomGenerator(); final int[] valuesClone = values.clone(); final List list = Utils.asList(valuesClone); Assert.assertNotNull(list); @@ -213,7 +212,7 @@ public class UtilsUnitTest extends BaseTest { // good. } } else { - final Random rdn = GenomeAnalysisEngine.getRandomGenerator(); + final Random rdn = Utils.getRandomGenerator(); final double[] valuesClone = values.clone(); final List list = Utils.asList(valuesClone); Assert.assertNotNull(list); diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java index 2087d9a0c..f0666aca2 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java @@ -32,13 +32,13 @@ package org.broadinstitute.gatk.utils.activeregion; import htsjdk.samtools.reference.ReferenceSequenceFile; import org.apache.commons.lang.ArrayUtils; import htsjdk.tribble.readers.LineIterator; +import org.broadinstitute.gatk.utils.variant.VCIterable; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.gatk.utils.variant.GATKVCFUtils; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFCodec; import htsjdk.variant.vcf.VCFHeader; @@ -270,7 +270,7 @@ public class BandPassActivityProfileUnitTest extends BaseTest { final File file = new File(path); final VCFCodec codec = new VCFCodec(); - final Pair> reader = GATKVCFUtils.readAllVCs(file, codec); + final Pair> reader = VCIterable.readAllVCs(file, codec); final List incRegions = new ArrayList(); final BandPassActivityProfile incProfile = new BandPassActivityProfile(genomeLocParser, null, MAX_PROB_PROPAGATION_DISTANCE, ACTIVE_PROB_THRESHOLD); diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java index 2d86f73c4..61d346d5a 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.downsampling; +package org.broadinstitute.gatk.utils.downsampling; import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; @@ -106,7 +106,7 @@ public class AlleleBiasedDownsamplingUtilsUnitTest extends BaseTest { actualCounts[2] += addG; actualCounts[3] += addT; - final int[] results = AlleleBiasedDownsamplingUtils.runSmartDownsampling(actualCounts, (int)(pileupSize * contaminationFraction)); + final int[] results = AlleleBiasedDownsamplingUtils.runSmartDownsampling(actualCounts, (int) (pileupSize * contaminationFraction)); Assert.assertTrue(countsAreEqual(results, targetCounts)); } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java index e9846da21..88b17c766 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java @@ -34,9 +34,6 @@ import org.apache.commons.io.FileUtils; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.IntervalBinding; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection; -import org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.GenomeLocSortedSet; @@ -81,12 +78,11 @@ public class IntervalUtilsUnitTest extends BaseTest { public void init() { File hg18Ref = new File(BaseTest.hg18Reference); try { - ReferenceDataSource referenceDataSource = new ReferenceDataSource(hg18Ref); + final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg18Ref); hg18Header = new SAMFileHeader(); - hg18Header.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()); - ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg18Ref); + hg18Header.setSequenceDictionary(seq.getSequenceDictionary()); hg18GenomeLocParser = new GenomeLocParser(seq); - hg18ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()).toList()) ; + hg18ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(seq.getSequenceDictionary()).toList()) ; } catch(FileNotFoundException ex) { throw new UserException.CouldNotReadInputFile(hg18Ref,ex); @@ -94,12 +90,11 @@ public class IntervalUtilsUnitTest extends BaseTest { File hg19Ref = new File(BaseTest.hg19Reference); try { - ReferenceDataSource referenceDataSource = new ReferenceDataSource(hg19Ref); + final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg19Ref); hg19Header = new SAMFileHeader(); - hg19Header.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()); - ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg19Ref); + hg19Header.setSequenceDictionary(seq.getSequenceDictionary()); hg19GenomeLocParser = new GenomeLocParser(seq); - hg19ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()).toList()) ; + hg19ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(seq.getSequenceDictionary()).toList()) ; hg19exomeIntervals = Collections.unmodifiableList(IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(hg19Intervals))); } @@ -1032,29 +1027,27 @@ public class IntervalUtilsUnitTest extends BaseTest { @Test(expectedExceptions=UserException.BadArgumentValue.class) public void testExceptionUponLegacyIntervalSyntax() throws Exception { - GenomeAnalysisEngine toolkit = new GenomeAnalysisEngine(); - toolkit.setGenomeLocParser(new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference)))); + final GenomeLocParser parser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference))); // Attempting to use the legacy -L "interval1;interval2" syntax should produce an exception: IntervalBinding binding = new IntervalBinding("1;2"); - binding.getIntervals(toolkit); + binding.getIntervals(parser); } @DataProvider(name="invalidIntervalTestData") public Object[][] invalidIntervalDataProvider() throws Exception { - GATKArgumentCollection argCollection = new GATKArgumentCollection(); File fastaFile = new File(publicTestDir + "exampleFASTA.fasta"); GenomeLocParser genomeLocParser = new GenomeLocParser(new IndexedFastaSequenceFile(fastaFile)); return new Object[][] { - new Object[] {argCollection, genomeLocParser, "chr1", 10000000, 20000000}, - new Object[] {argCollection, genomeLocParser, "chr2", 1, 2}, - new Object[] {argCollection, genomeLocParser, "chr1", -1, 50} + new Object[] {genomeLocParser, "chr1", 10000000, 20000000}, + new Object[] {genomeLocParser, "chr2", 1, 2}, + new Object[] {genomeLocParser, "chr1", -1, 50} }; } @Test(dataProvider="invalidIntervalTestData") - public void testInvalidPicardIntervalHandling(GATKArgumentCollection argCollection, GenomeLocParser genomeLocParser, + public void testInvalidPicardIntervalHandling(GenomeLocParser genomeLocParser, String contig, int intervalStart, int intervalEnd ) throws Exception { SAMFileHeader picardFileHeader = new SAMFileHeader(); @@ -1068,11 +1061,11 @@ public class IntervalUtilsUnitTest extends BaseTest { List> intervalArgs = new ArrayList>(1); intervalArgs.add(new IntervalBinding(picardIntervalFile.getAbsolutePath())); - IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalArguments.intervalSetRule, argCollection.intervalArguments.intervalMerging, argCollection.intervalArguments.intervalPadding, genomeLocParser); + IntervalUtils.loadIntervals(intervalArgs, IntervalSetRule.UNION, IntervalMergingRule.ALL, 0, genomeLocParser); } @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData") - public void testInvalidGATKFileIntervalHandling(GATKArgumentCollection argCollection, GenomeLocParser genomeLocParser, + public void testInvalidGATKFileIntervalHandling(GenomeLocParser genomeLocParser, String contig, int intervalStart, int intervalEnd ) throws Exception { File gatkIntervalFile = createTempFile("testInvalidGATKFileIntervalHandling", ".intervals", @@ -1081,7 +1074,7 @@ public class IntervalUtilsUnitTest extends BaseTest { List> intervalArgs = new ArrayList>(1); intervalArgs.add(new IntervalBinding(gatkIntervalFile.getAbsolutePath())); - IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalArguments.intervalSetRule, argCollection.intervalArguments.intervalMerging, argCollection.intervalArguments.intervalPadding, genomeLocParser); + IntervalUtils.loadIntervals(intervalArgs, IntervalSetRule.UNION, IntervalMergingRule.ALL, 0, genomeLocParser); } private File createTempFile( String tempFilePrefix, String tempFileExtension, String... lines ) throws Exception { diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java index 13a2e8a1d..46b2e949f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java @@ -35,7 +35,7 @@ import java.util.Arrays; import java.util.List; import java.util.Random; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.Assert; @@ -315,8 +315,8 @@ public class IOUtilsUnitTest extends BaseTest { } private byte[] getDeterministicRandomData ( int size ) { - GenomeAnalysisEngine.resetRandomGenerator(); - Random rand = GenomeAnalysisEngine.getRandomGenerator(); + Utils.resetRandomGenerator(); + Random rand = Utils.getRandomGenerator(); byte[] randomData = new byte[size]; rand.nextBytes(randomData); diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java index 1f02a68e5..0d06c61c6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java @@ -28,7 +28,7 @@ package org.broadinstitute.gatk.utils.locusiterator; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; import htsjdk.samtools.SAMFileHeader; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.Utils; @@ -104,7 +104,7 @@ public class LocusIteratorBenchmark extends SimpleBenchmark { final org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState libs = new org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState( new LocusIteratorByStateBaseTest.FakeCloseableIterator(reads.iterator()), - LocusIteratorByStateBaseTest.createTestReadProperties(), + null, true, false, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups()); diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java index 286c7120c..073d69cde 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java @@ -28,12 +28,7 @@ package org.broadinstitute.gatk.utils.locusiterator; import htsjdk.samtools.*; import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; -import org.broadinstitute.gatk.engine.filters.ReadFilter; -import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.Utils; @@ -57,34 +52,19 @@ public class LocusIteratorByStateBaseTest extends BaseTest { genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); } - protected LocusIteratorByState makeLTBS(List reads, - ReadProperties readAttributes) { + protected LocusIteratorByState makeLTBS(List reads) { + return makeLTBS(reads, null, false); + } + + protected LocusIteratorByState makeLTBS(final List reads, + final DownsamplingMethod downsamplingMethod, + final boolean keepUniqueReadList) { return new LocusIteratorByState(new FakeCloseableIterator(reads.iterator()), - readAttributes, + downsamplingMethod, true, keepUniqueReadList, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups()); } - public static ReadProperties createTestReadProperties() { - return createTestReadProperties(null, false); - } - - public static ReadProperties createTestReadProperties( DownsamplingMethod downsamplingMethod, final boolean keepReads ) { - return new ReadProperties( - Collections.emptyList(), - new SAMFileHeader(), - SAMFileHeader.SortOrder.coordinate, - false, - ValidationStringency.STRICT, - downsamplingMethod, - new ValidationExclusion(), - Collections.emptyList(), - Collections.emptyList(), - true, - (byte) -1, - keepReads); - } - public static class FakeCloseableIterator implements CloseableIterator { Iterator iterator; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java index 08cbecaf8..cbbdf3609 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java @@ -28,10 +28,9 @@ package org.broadinstitute.gatk.utils.locusiterator; import htsjdk.samtools.CigarOperator; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; -import org.broadinstitute.gatk.engine.ReadProperties; -import org.broadinstitute.gatk.engine.contexts.AlignmentContext; -import org.broadinstitute.gatk.engine.downsampling.DownsampleType; -import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.downsampling.DownsampleType; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.utils.NGSPlatform; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.Utils; @@ -69,7 +68,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { List reads = Arrays.asList(mapped1, unmapped, allI, mapped2); // create the iterator by state with the fake reads and fake records - li = makeLTBS(reads,createTestReadProperties(DownsamplingMethod.NONE, true)); + li = makeLTBS(reads, DownsamplingMethod.NONE, true); Assert.assertTrue(li.hasNext()); AlignmentContext context = li.next(); @@ -85,9 +84,6 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { final byte[] bases1 = new byte[] {'A','A','A','A','A','A','A','A','A','A'}; final byte[] bases2 = new byte[] {'A','A','A','C','A','A','A','A','A','C'}; - // create a test version of the Reads object - ReadProperties readAttributes = createTestReadProperties(); - GATKSAMRecord r1 = ArtificialSAMUtils.createArtificialRead(header,"r1",0,1,10); r1.setReadBases(bases1); r1.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20}); @@ -111,7 +107,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { List reads = Arrays.asList(r1, r2, r3, r4); // create the iterator by state with the fake reads and fake records - li = makeLTBS(reads,readAttributes); + li = makeLTBS(reads); while (li.hasNext()) { AlignmentContext context = li.next(); @@ -125,9 +121,6 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'}; final byte[] indelBases = new byte[] {'A','A','A','A','C','T','A','A','A','A','A','A'}; - // create a test version of the Reads object - ReadProperties readAttributes = createTestReadProperties(); - GATKSAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10); before.setReadBases(bases); before.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20}); @@ -146,7 +139,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { List reads = Arrays.asList(before, during, after); // create the iterator by state with the fake reads and fake records - li = makeLTBS(reads,readAttributes); + li = makeLTBS(reads); boolean foundIndel = false; while (li.hasNext()) { @@ -170,9 +163,6 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { public void testWholeIndelReadInIsolation() { final int firstLocus = 44367789; - // create a test version of the Reads object - ReadProperties readAttributes = createTestReadProperties(); - GATKSAMRecord indelOnlyRead = ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, firstLocus, 76); indelOnlyRead.setReadBases(Utils.dupBytes((byte)'A',76)); indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76)); @@ -181,7 +171,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { List reads = Arrays.asList(indelOnlyRead); // create the iterator by state with the fake reads and fake records - li = makeLTBS(reads, readAttributes); + li = makeLTBS(reads); // Traditionally, reads that end with indels bleed into the pileup at the following locus. Verify that the next pileup contains this read // and considers it to be an indel-containing read. @@ -219,7 +209,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { List reads = Arrays.asList(leadingRead, indelOnlyRead, fullMatchAfterIndel); // create the iterator by state with the fake reads and fake records - li = makeLTBS(reads, createTestReadProperties()); + li = makeLTBS(reads, null, false); int currentLocus = firstLocus; int numAlignmentContextsFound = 0; @@ -260,7 +250,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { List reads = Arrays.asList(read1); // create the iterator by state with the fake reads and fake records - li = makeLTBS(reads, createTestReadProperties()); + li = makeLTBS(reads, null, false); while(li.hasNext()) { AlignmentContext alignmentContext = li.next(); @@ -281,7 +271,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { reads = Arrays.asList(read2); // create the iterator by state with the fake reads and fake records - li = makeLTBS(reads, createTestReadProperties()); + li = makeLTBS(reads, null, false); while(li.hasNext()) { AlignmentContext alignmentContext = li.next(); @@ -329,7 +319,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { @Test(enabled = true && ! DEBUG, dataProvider = "IndelLengthAndBasesTest") public void testIndelLengthAndBasesTest(GATKSAMRecord read, final CigarOperator op, final int eventSize, final String eventBases) { // create the iterator by state with the fake reads and fake records - li = makeLTBS(Arrays.asList((GATKSAMRecord)read), createTestReadProperties()); + li = makeLTBS(Arrays.asList((GATKSAMRecord)read), null, false); Assert.assertTrue(li.hasNext()); @@ -381,7 +371,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { public void testLIBS(LIBSTest params) { // create the iterator by state with the fake reads and fake records final GATKSAMRecord read = params.makeRead(); - li = makeLTBS(Arrays.asList((GATKSAMRecord)read), createTestReadProperties()); + li = makeLTBS(Arrays.asList((GATKSAMRecord)read), null, false); final LIBS_position tester = new LIBS_position(read); int bpVisited = 0; @@ -482,7 +472,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { final List reads = bamBuilder.makeReads(); li = new LocusIteratorByState(new FakeCloseableIterator(reads.iterator()), - createTestReadProperties(downsampler, keepReads), + downsampler, true, keepReads, genomeLocParser, bamBuilder.getSamples()); @@ -643,7 +633,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { final WeakReadTrackingIterator iterator = new WeakReadTrackingIterator(nReadsPerLocus, readLength, payloadInBytes, header); li = new LocusIteratorByState(iterator, - createTestReadProperties(downsampler, false), + downsampler, true, false, genomeLocParser, samples); @@ -734,7 +724,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { public void testAdapterClipping(final int nClipsOnLeft, final int nReadContainingPileups, final int nClipsOnRight, final GATKSAMRecord read) { li = new LocusIteratorByState(new FakeCloseableIterator<>(Collections.singletonList(read).iterator()), - createTestReadProperties(DownsamplingMethod.NONE, false), + DownsamplingMethod.NONE, true, false, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups()); diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java index f25ab8d58..62a704217 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata; +package org.broadinstitute.gatk.utils.refdata; import htsjdk.samtools.SAMFileHeader; import org.apache.log4j.Logger; @@ -31,10 +31,10 @@ import htsjdk.tribble.Feature; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.RodBinding; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.codecs.table.TableFeature; -import org.broadinstitute.gatk.engine.refdata.utils.GATKFeature; -import org.broadinstitute.gatk.engine.refdata.utils.RODRecordList; +import org.broadinstitute.gatk.utils.refdata.utils.GATKFeature; +import org.broadinstitute.gatk.utils.refdata.utils.RODRecordList; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java index ec3b470f8..b0805e161 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.tracks; +package org.broadinstitute.gatk.utils.refdata.tracks; import htsjdk.samtools.reference.IndexedFastaSequenceFile; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java index a64773af8..5019e78e7 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.tracks; +package org.broadinstitute.gatk.utils.refdata.tracks; import htsjdk.samtools.reference.IndexedFastaSequenceFile; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java index e77c0797e..cee60aace 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.tribble.CloseableTribbleIterator; import htsjdk.tribble.Feature; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java index d95c320cb..768bf50df 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.tribble.Feature; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java index 7aa07ef58..34129abc8 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMSequenceDictionary; import org.testng.Assert; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.refdata.ReferenceOrderedDatum; +import org.broadinstitute.gatk.utils.refdata.ReferenceOrderedDatum; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java index 90b5e7a35..190ec846b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.tribble.Feature; import htsjdk.tribble.FeatureCodec; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java index 17179f3ba..2750e271e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java @@ -23,16 +23,15 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.refdata.utils; +package org.broadinstitute.gatk.utils.refdata.utils; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.tribble.FeatureCodec; -import htsjdk.tribble.Tribble; import htsjdk.tribble.index.Index; -import org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager; -import org.broadinstitute.gatk.engine.refdata.tracks.IndexDictionaryUtils; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrack; -import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder; +import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager; +import org.broadinstitute.gatk.utils.refdata.tracks.IndexDictionaryUtils; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack; +import org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder; import org.broadinstitute.gatk.utils.GenomeLocParser; import java.io.File; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java index c28e901d2..fa34fb71b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java @@ -23,9 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.gatk.engine.report; +package org.broadinstitute.gatk.utils.report; import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportColumn; +import org.broadinstitute.gatk.utils.report.GATKReportTable; +import org.broadinstitute.gatk.utils.report.GATKReportVersion; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java index 48ad2129d..a4e6be203 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.gatk.utils.sam; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; import static org.testng.Assert.fail; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java index 271a75ad9..4117f7487 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java @@ -27,7 +27,7 @@ package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMReadGroupRecord; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.testng.annotations.Test; import org.testng.annotations.DataProvider; @@ -76,7 +76,7 @@ public class ArtificialSingleSampleReadStreamUnitTest extends BaseTest { readGroup.setSample("testSample"); header.addReadGroup(readGroup); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); // brute force testing! for ( int numContigs = 0; numContigs <= 2; numContigs++ ) { @@ -123,7 +123,7 @@ public class ArtificialSingleSampleReadStreamUnitTest extends BaseTest { public void testArtificialSingleSampleReadStream( ArtificialSingleSampleReadStreamTest test ) { logger.warn("Running test: " + test); - GenomeAnalysisEngine.resetRandomGenerator(); + Utils.resetRandomGenerator(); test.run(); } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java index c7ceea10a..14b56718e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java @@ -28,7 +28,6 @@ package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; @@ -189,7 +188,7 @@ public class ReadUtilsUnitTest extends BaseTest { @Test (enabled = true) public void testGetBasesReverseComplement() { int iterations = 1000; - Random random = GenomeAnalysisEngine.getRandomGenerator(); + Random random = Utils.getRandomGenerator(); while(iterations-- > 0) { final int l = random.nextInt(1000); GATKSAMRecord read = GATKSAMRecord.createRandomRead(l); diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java index 086cefed7..ac301ce37 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java @@ -28,14 +28,12 @@ package org.broadinstitute.gatk.utils.text; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.commandline.ParsingEngine; import org.broadinstitute.gatk.utils.commandline.Tags; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.File; -import java.io.PrintWriter; import java.util.*; /** @@ -146,10 +144,7 @@ public class ListFileUtilsUnitTest extends BaseTest { List bamFiles = new ArrayList(); bamFiles.add(tempListFile.getAbsolutePath()); - CommandLineGATK testInstance = new CommandLineGATK(); - testInstance.setParser(new ParsingEngine(testInstance)); - - List unpackedBAMFileList = ListFileUtils.unpackBAMFileList(bamFiles,new ParsingEngine(testInstance)); + List unpackedBAMFileList = ListFileUtils.unpackBAMFileList(bamFiles,new ParsingEngine(null)); Assert.assertEquals(unpackedBAMFileList.size(), expectedUnpackedFileList.size(), "Unpacked BAM file list contains extraneous lines"); diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java index feb10a7d4..860c54736 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java @@ -26,7 +26,6 @@ package org.broadinstitute.gatk.utils.variant; import htsjdk.variant.variantcontext.*; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; @@ -1100,8 +1099,8 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest { } private static GenotypesContext createGenotypesContext(final int numGenotypes, final List alleles) { - GenomeAnalysisEngine.resetRandomGenerator(); - final Random random = GenomeAnalysisEngine.getRandomGenerator(); + Utils.resetRandomGenerator(); + final Random random = Utils.getRandomGenerator(); final GenotypesContext gc = GenotypesContext.create(); for ( int i = 0; i < numGenotypes; i++ ) { @@ -1585,7 +1584,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest { @DataProvider(name="totalPloidyData") public Object[][] totalPloidyData() { - final Random rdn = GenomeAnalysisEngine.getRandomGenerator(); + final Random rdn = Utils.getRandomGenerator(); final List resultList = new ArrayList<>(); for (int i = 0; i < 100; i++) { final int sampleCount = rdn.nextInt(10); diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml index b4c5491b6..a4ce50873 100644 --- a/public/package-tests/pom.xml +++ b/public/package-tests/pom.xml @@ -35,7 +35,7 @@ - ${gatk.basedir}/public/gatk-tools-public/target/gatk-tools-public-${project.version}-tests.jar + ${gatk.basedir}/public/gatk-utils/target/gatk-utils-${project.version}-tests.jar + ${gatk.basedir}/public/gatk-engine/target/gatk-engine-${project.version}-tests.jar ${gatk.basedir}/public/gatk-queue/target/gatk-queue-${project.version}-tests.jar @@ -143,7 +144,8 @@ ${gatk.packagetests.testClasses} - ${gatk.basedir}/public/gatk-tools-public/target/gatk-tools-public-${project.version}-tests.jar + ${gatk.basedir}/public/gatk-utils/target/gatk-utils-${project.version}-tests.jar + ${gatk.basedir}/public/gatk-engine/target/gatk-engine-${project.version}-tests.jar ${gatk.basedir}/public/gatk-queue/target/gatk-queue-${project.version}-tests.jar