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Split all imports of tools|engine from utils, and all tools from engine. 

Second of two commits, modifying actual files.
This commit is contained in:
Khalid Shakir 2014-10-22 00:40:45 +08:00
parent bb7151192a
commit 5c9fe1a06d
596 changed files with 3184 additions and 2508 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
pom.xml
View File

@ -173,7 +173,7 @@
<outputDirectory>${project.reporting.outputDirectory}/apidocs</outputDirectory>
<resources>
<resource>
<directory>${gatk.basedir}/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help</directory>
<directory>${gatk.basedir}/public/gatk-utils/src/main/config/org/broadinstitute/gatk/utils/help</directory>
</resource>
</resources>
</configuration>
@ -198,8 +198,7 @@
<docletPath>${project.build.outputDirectory}</docletPath>
<docletArtifact>
<groupId>${project.groupId}</groupId>
<!-- TODO: THIS IS SUPPOSED TO BE GATK-UTILS! -->
<artifactId>gatk-tools-public</artifactId>
<artifactId>gatk-utils</artifactId>
<version>${project.version}</version>
</docletArtifact>
<maxmemory>2g</maxmemory>
@ -689,7 +688,7 @@
<!-- Only generate the GATK Docs across the parent aggregation, not the children too. -->
<inherited>false</inherited>
<configuration>
<doclet>org.broadinstitute.gatk.utils.help.GATKDoclet</doclet>
<doclet>org.broadinstitute.gatk.tools.walkers.help.WalkerDoclet</doclet>
<docletArtifact>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-package-distribution</artifactId>

7
protected/gatk-package-distribution/pom.xml
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@ -43,6 +43,11 @@
<artifactId>gatk-tools-protected</artifactId>
<version>${project.version}</version>
</dependency>
<!-- slf4j bindings must only be at the package level: http://www.slf4j.org/manual.html -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</dependency>
<!-- Tribble codecs & the variant package (VCF, BCF, and VariantContext) -->
<dependency>
<groupId>samtools</groupId>
@ -73,7 +78,7 @@
<!-- Required for binary-dist assembly, excluded by shade -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-engine</artifactId>
<artifactId>gatk-utils</artifactId>
<version>${project.version}</version>
<classifier>example-resources</classifier>
<type>tar.bz2</type>

6
protected/gatk-queue-extensions-distribution/pom.xml
View File

@ -41,6 +41,10 @@
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</dependency>
<dependency>
<groupId>picard</groupId>
<artifactId>picard</artifactId>
</dependency>
<!--
Extensions generator dependency only applies to the exec:exec,
not the artifact, but don't know another way to include
@ -66,7 +70,7 @@
-->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-tools-public</artifactId>
<artifactId>gatk-utils</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>

2
protected/gatk-queue-package-distribution/pom.xml
View File

@ -80,7 +80,7 @@
<!-- Required for binary-dist assembly, excluded by shade -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-engine</artifactId>
<artifactId>gatk-utils</artifactId>
<version>${project.version}</version>
<classifier>example-resources</classifier>
<type>tar.bz2</type>

10
protected/gatk-tools-protected/pom.xml
View File

@ -48,7 +48,15 @@
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-tools-public</artifactId>
<artifactId>gatk-utils</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-engine</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>

5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java
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@ -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;

5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java
View File

@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java
View File

@ -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;

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java
View File

@ -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;

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java
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@ -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.

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java
View File

@ -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

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java
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@ -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;

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java
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@ -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;

7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java
View File

@ -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 <code>null</code>, but a zero-size collection if there are no differences.
*/
@Requires("other != null && thisRole != null && otherRole != null && !thisRole.equalsIgnoreCase(otherRole)")
Map<String,? extends CharSequence> compareReportArguments(final RecalibrationArgumentCollection other,final String thisRole, final String otherRole) {
public Map<String,? extends CharSequence> compareReportArguments(final RecalibrationArgumentCollection other,final String thisRole, final String otherRole) {
final Map<String,String> 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);

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java
View File

@ -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.*;

5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java
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@ -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;
/*

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java
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@ -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]

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java
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@ -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.

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java
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@ -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]

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java
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@ -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]

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java
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@ -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;

7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java
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@ -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.*;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java
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@ -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;

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java
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@ -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.*;

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java
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@ -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;

7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java
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@ -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;

9
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java
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@ -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;

7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java
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@ -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;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java
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@ -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;

9
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java
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@ -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;

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java
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@ -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;
}
}

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java
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@ -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;

7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java
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@ -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;

7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java
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@ -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;

12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java
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@ -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;

7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java
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@ -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;
/**

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java
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@ -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;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java
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@ -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;

12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
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@ -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<Long, Long> {
intervalListIterator = new PeekableIterator<GenomeLoc>(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.

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java
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@ -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;

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java
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@ -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;

1
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java
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@ -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;

7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java
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@ -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;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
View File

@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
View File

@ -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;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
View File

@ -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;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
View File

@ -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;

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
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@ -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;

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java
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@ -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.

11
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java
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@ -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;

1
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java
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@ -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.

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java
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@ -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.

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -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;

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java
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@ -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.
*

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -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;

5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java
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@ -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;

16
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java
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@ -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<List<VariantCallContext>, 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);
}

9
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java
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@ -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;

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java
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@ -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;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java
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@ -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.

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
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@ -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;

23
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -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<List<VariantContext>, 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);
}

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
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@ -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;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
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@ -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;

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java
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@ -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.*;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java
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@ -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;

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java
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@ -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;

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java
View File

@ -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;

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
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@ -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] );
}

10
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
View File

@ -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<Haplotype> haplotypes = new IndexedAlleleList<>(assemblyResultSet.getHaplotypeList());
final ReadLikelihoods result = new ReadLikelihoods(samples, haplotypes, reads);
final Map<Haplotype,Allele> 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++) {

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java
View File

@ -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;

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java
View File

@ -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;

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