From eacf205f4079e55ed03dd248cbb8c1a41491c01e Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sat, 16 Jul 2011 09:22:34 -0400 Subject: [PATCH 20/39] Tests needed to be updated to reflect the code reorg of tribble. --- .../org/broadinstitute/sting/WalkerTest.java | 21 +++++++++++-------- .../codecs/vcf/IndexFactoryUnitTest.java | 3 ++- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java index d65f4ec34..a39fa37fe 100755 --- a/public/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java @@ -65,19 +65,22 @@ public class WalkerTest extends BaseTest { throw new StingException("Found an index created for file " + resultFile + " but we can only validate VCF files. Extend this code!"); } - System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile); - Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec()); - Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath()); - - if ( ! indexFromOutputFile.equals(dynamicIndex) ) { - Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed. FileIndex %s vs. on-the-fly %s%n", - indexFromOutputFile.getProperties(), - dynamicIndex.getProperties())); - } + assertOnDiskIndexEqualToNewlyCreatedIndex(indexFile, name, resultFile); } } + public static void assertOnDiskIndexEqualToNewlyCreatedIndex(final File indexFile, final String name, final File resultFile) { + System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile); + Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec()); + Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath()); + + if ( ! indexFromOutputFile.equals(dynamicIndex) ) { + Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed. FileIndex %s vs. on-the-fly %s%n", + indexFromOutputFile.getProperties(), + dynamicIndex.getProperties())); + } + } public List assertMatchingMD5s(final String name, List resultFiles, List expectedMD5s) { List md5s = new ArrayList(); diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java index 2f6b589f4..68a2ecf8d 100755 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java @@ -4,6 +4,7 @@ import org.broad.tribble.Tribble; import org.broad.tribble.index.*; import org.broad.tribble.iterators.CloseableTribbleIterator; import org.broad.tribble.source.BasicFeatureSource; +import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.Test; @@ -75,7 +76,7 @@ public class IndexFactoryUnitTest { // test that the input index is the same as the one created from the identical input file // test that the dynamic index is the same as the output index, which is equal to the input index - Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(outputFile, outputFileIndex, new VCFCodec())); + WalkerTest.assertOnDiskIndexEqualToNewlyCreatedIndex(outputFileIndex, "unittest", outputFile); } } } From 07b875c7796972eff2c56c662f198821a5c4e659 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Sat, 16 Jul 2011 09:57:46 -0400 Subject: [PATCH 21/39] Renaming the updated tribble jar file to match the svn revision number. --- .../org.broad/{tribble-4.jar => tribble-14.jar} | Bin .../org.broad/{tribble-4.xml => tribble-14.xml} | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename settings/repository/org.broad/{tribble-4.jar => tribble-14.jar} (100%) rename settings/repository/org.broad/{tribble-4.xml => tribble-14.xml} (57%) diff --git a/settings/repository/org.broad/tribble-4.jar b/settings/repository/org.broad/tribble-14.jar similarity index 100% rename from settings/repository/org.broad/tribble-4.jar rename to settings/repository/org.broad/tribble-14.jar diff --git a/settings/repository/org.broad/tribble-4.xml b/settings/repository/org.broad/tribble-14.xml similarity index 57% rename from settings/repository/org.broad/tribble-4.xml rename to settings/repository/org.broad/tribble-14.xml index 07235efb0..f2116324a 100644 --- a/settings/repository/org.broad/tribble-4.xml +++ b/settings/repository/org.broad/tribble-14.xml @@ -1,4 +1,4 @@ - From 2b55d5b7c0dfca0abd09ab810206d5a437d598ec Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sat, 16 Jul 2011 16:45:55 -0400 Subject: [PATCH 22/39] Test tribble library where equals() ignores time stamps. --- settings/repository/org.broad/tribble-14.jar | Bin 286423 -> 286358 bytes 1 file changed, 0 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z$;X2I!ZvO9TY!gGbCg<~50Pa@TEV{(sKiNzPgVY%Q&czc+JP~!XHmCSaQreh#W^|J zto}BfGuG&*?R6#>7HFN+!Lc9@8fcT}4beklHA4-VXn3>_s)ehgS|XhQ9bVf*3sM57(& ztAt5LxwZgXoMd!WH7{$Xs+wf<){dQvAo0pQ83yfm$42H&Hil~1??omab!oEEM>BtC zBUR_MI5ltz1g`%+qQa&23X-9zO;e44x;h0GO|vF_Rh6zMs7X^n9^w}A0`0x-(r2p6 z-SuSkO<(M+Z!va#vX{W=>Tq8@T0K$>fzX4tzMCWTG`0Id-K8c?19!y`y>*0tG$g|1 zQGH7wcVwK6TrGmgW!*hu9qq<_;CJ<-m#(M%{g{g()wq+Su^_;nkpx{mExE_?hdJt3y0JYQ8gvv9VK zxMlOr`zLfAnFSX;)`G;U%YTFA2#sH*&c^a<{t@AhRb{iWPHe2&J=>V3ed3coLw)2! zsaSsNJO=_NQ*1b)Mvqbp=Rn|*OhM9A Date: Sun, 17 Jul 2011 10:14:23 -0400 Subject: [PATCH 23/39] Moved the varianteval/tags/DataPoint.java and varianteval/tags/Analysis.java to varianteval/utils. This allows rsync to see these files with the -C option, as tags is some kind of reserved CVS keyword. --- .../gatk/walkers/varianteval/VariantEvalWalker.java | 5 ++--- .../walkers/varianteval/evaluators/CompOverlap.java | 4 ++-- .../walkers/varianteval/evaluators/CountVariants.java | 4 ++-- .../varianteval/evaluators/GenotypeConcordance.java | 4 ++-- .../evaluators/GenotypePhasingEvaluator.java | 7 +++---- .../varianteval/evaluators/IndelLengthHistogram.java | 4 ++-- .../varianteval/evaluators/IndelMetricsByAC.java | 4 ++-- .../varianteval/evaluators/IndelStatistics.java | 4 ++-- .../evaluators/MendelianViolationEvaluator.java | 10 ++-------- .../varianteval/evaluators/PrintMissingComp.java | 4 ++-- .../varianteval/evaluators/SimpleMetricsByAC.java | 7 +++---- .../varianteval/evaluators/ThetaVariantEvaluator.java | 4 ++-- .../varianteval/evaluators/TiTvVariantEvaluator.java | 4 ++-- .../varianteval/evaluators/ValidationReport.java | 5 ++--- .../varianteval/evaluators/VariantQualityScore.java | 4 ++-- .../walkers/varianteval/{tags => util}/Analysis.java | 2 +- .../varianteval/util/AnalysisModuleScanner.java | 2 -- .../walkers/varianteval/{tags => util}/DataPoint.java | 2 +- .../walkers/varianteval/util/VariantEvalUtils.java | 3 --- 19 files changed, 34 insertions(+), 49 deletions(-) rename public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/{tags => util}/Analysis.java (80%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/{tags => util}/DataPoint.java (77%) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 15d808ebe..c9c5e09a8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -20,7 +20,7 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.*; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator; @@ -30,10 +30,9 @@ import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import net.sf.picard.reference.FastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import net.sf.picard.reference.ReferenceSequence; + import java.io.FileNotFoundException; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index 76db330ed..85373baa8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -1,12 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; /** * The Broad Institute diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index c4277adc9..befb2ff13 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -1,12 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @Analysis(description = "Counts different classes of variants in the sample") diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java index 4b56cf130..58803c9d0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java @@ -1,14 +1,14 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java index 3d14dd0e5..407b71893 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java @@ -1,6 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.*; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -9,10 +10,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.phasing.AllelePair; import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index 5daf33a9f..f7f9fce0c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -1,11 +1,11 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java index eca6c5193..dd4bb492e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java @@ -1,12 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java index 48b06d532..1bd420e0a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.IndelUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 85e0b5889..16ec74433 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -1,22 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.MendelianViolation; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.Arrays; -import java.util.List; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - /** * Mendelian violation detection and counting *

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java index 7d54d0df8..e83914ef8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java @@ -24,12 +24,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites") public class PrintMissingComp extends VariantEvaluator { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java index deed05508..395309975 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.*; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -8,11 +9,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import java.util.ArrayList; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index 89c67cfe9..f9cda5e0b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index 8811dc001..deeafd851 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -1,12 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.BaseUtils; @Analysis(description = "Ti/Tv Variant Evaluator") diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index 405f35635..756427581 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -1,14 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java index 4af14810b..29a61e27a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java @@ -25,14 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.collections.Pair; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java similarity index 80% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java index 129d5a95d..2b37ce210 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.varianteval.tags; +package org.broadinstitute.sting.gatk.walkers.varianteval.util; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java index c8d917040..db44e9e28 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java @@ -23,8 +23,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.annotation.Annotation; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java similarity index 77% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java index 3ba448049..396843252 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.varianteval.tags; +package org.broadinstitute.sting.gatk.walkers.varianteval.util; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index b8e45e462..eabd2e588 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -7,15 +7,12 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; -import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; From a5bfcb1ed9f4ee0f5a94a744bd9e31bbd8d254a2 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 17 Jul 2011 10:25:34 -0400 Subject: [PATCH 24/39] V15 is broken. 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zwa6dso54WToZ5`@wjVOzfw5LKpkz6!)n5>E#uzQcsnNb+e~`WT7iDj<$oxeQ6Wzx6 zh8>zb=hX^SWb#4c@c*k>()kZbuYPeZc8!66_brh))=2c9U+l#fyYg+Z0t-(*O$BU; zko2~IF=HWMHjZ>sz++>L=E|NI+`X2CA+F`q)aW@WlC*_*E!GGXSH~J*Npf@dYX<;- ymi7IUIZL!RM1`qGi)-x-Qw$#GoA^!Rurxkwgi8<;+T$;B`^Om}&ZJD_WBNZ`r6S7! diff --git a/settings/repository/org.broad/tribble-14.xml b/settings/repository/org.broad/tribble-15.xml similarity index 59% rename from settings/repository/org.broad/tribble-14.xml rename to settings/repository/org.broad/tribble-15.xml index f2116324a..e23eec339 100644 --- a/settings/repository/org.broad/tribble-14.xml +++ b/settings/repository/org.broad/tribble-15.xml @@ -1,4 +1,4 @@ - From 1af76736b9dc41da345df90648ec5d74ade03f70 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Sun, 17 Jul 2011 11:41:34 -0400 Subject: [PATCH 25/39] Guarantees that the list of files will always be in the same order. --- .../src/org/broadinstitute/sting/queue/util/QScriptUtils.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala index 9fb4fa30d..99aaa9474 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala @@ -31,7 +31,7 @@ object QScriptUtils { for (bam <- fromFile(in).getLines) if (!bam.startsWith("#") && !bam.isEmpty ) list :+= new File(bam.trim()) - list + list.sortWith(_.compareTo(_) < 0) } /** From 4db2b13e9ebd54f832d05f885d7ec8946118fb70 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 17 Jul 2011 13:05:04 -0400 Subject: [PATCH 26/39] Rev tribble. Just added more documentation for diffEngine and pointer to new wiki: http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine --- .../gatk/walkers/diffengine/DiffEngine.java | 2 +- .../walkers/diffengine/DiffableReader.java | 15 +++++++++++++++ .../org/broadinstitute/sting/WalkerTest.java | 2 +- settings/repository/org.broad/tribble-15.jar | Bin 286159 -> 0 bytes .../{tribble-15.xml => tribble-16.xml} | 0 5 files changed, 17 insertions(+), 2 deletions(-) delete mode 100644 settings/repository/org.broad/tribble-15.jar rename settings/repository/org.broad/{tribble-15.xml => tribble-16.xml} (100%) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java index 6d85df71d..2f87a900a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java @@ -209,7 +209,7 @@ public class DiffEngine { protected void printSummaryReport(List sortedSummaries, SummaryReportParams params ) { GATKReport report = new GATKReport(); final String tableName = "diffences"; - report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffObjectsWalker_and_SummarizedDifferences for more information"); + report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information"); GATKReportTable table = report.getTable(tableName); table.addPrimaryKey("Difference", true); table.addColumn("NumberOfOccurrences", 0); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java index af5771c55..a117206f1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java @@ -39,12 +39,27 @@ import java.io.File; */ public interface DiffableReader { @Ensures("result != null") + /** + * Return the name of this DiffableReader type. For example, the VCF reader returns 'VCF' and the + * bam reader 'BAM' + */ public String getName(); @Ensures("result != null") @Requires("file != null") + /** + * Read up to maxElementsToRead DiffElements from file, and return them. + */ public DiffElement readFromFile(File file, int maxElementsToRead); + /** + * Return true if the file can be read into DiffElement objects with this reader. This should + * be uniquely true/false for all readers, as the system will use the first reader that can read the + * file. This routine should never throw an exception. The VCF reader, for example, looks at the + * first line of the file for the ##format=VCF4.1 header, and the BAM reader for the BAM_MAGIC value + * @param file + * @return + */ @Requires("file != null") public boolean canRead(File file); } diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java index a39fa37fe..22635dfa3 100755 --- a/public/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java @@ -75,7 +75,7 @@ public class WalkerTest extends BaseTest { Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec()); Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath()); - if ( ! indexFromOutputFile.equals(dynamicIndex) ) { + if ( ! indexFromOutputFile.equalsIgnoreTimestamp(dynamicIndex) ) { Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed. 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9ca9cf52aca2fe7bc47c6cc5d7eb527a77c488a6 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 17 Jul 2011 15:38:33 -0400 Subject: [PATCH 28/39] Uncommenting a stray commented test. --- .../walkers/variantutils/CombineVariantsIntegrationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index daaab9425..fb18c6c33 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -119,7 +119,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec); } -// @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); } + @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); } @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "df96cb3beb2dbb5e02f80abec7d3571e"); } @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "f72a178137e25dbe0b931934cdc0079d"); } @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "f704caeaaaed6711943014b847fe381a"); } From 4ea433f8e1083bb79416dd326b7e7feecfd188a4 Mon Sep 17 00:00:00 2001 From: Kiran V Garimella Date: Sun, 17 Jul 2011 19:42:00 -0400 Subject: [PATCH 31/39] Moved PhaseByTransmission to public --- .../walkers/phasing/PhaseByTransmission.java | 321 ++++++++++++++++++ 1 file changed, 321 insertions(+) create mode 100755 public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java new file mode 100755 index 000000000..523c24d9b --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -0,0 +1,321 @@ +package org.broadinstitute.sting.gatk.walkers.phasing; + +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; + +import java.util.*; + +/** + * Phases a trio VCF (child phased by transmission, implied phase carried over to parents). Given genotypes for a trio, + * this walker modifies the genotypes (if necessary) to reflect the most likely configuration given the genotype + * likelihoods and inheritance constraints, phases child by transmission and carries over implied phase to the parents + * (their alleles in their genotypes are ordered as transmitted|untransmitted). Computes probability that the + * determined phase is correct given that the genotype configuration is correct (useful if you want to use this to + * compare phasing accuracy, but want to break that comparison down by phasing confidence in the truth set). Optionally + * filters out sites where the phasing is indeterminate (site has no-calls), ambiguous (everyone is heterozygous), or + * the genotypes exhibit a Mendelian violation. This walker assumes there are only three samples in the VCF file to + * begin. + */ +public class PhaseByTransmission extends RodWalker { + @Argument(shortName="f", fullName="familyPattern", required=true, doc="Pattern for the family structure (usage: mom+dad=child)") + public String familyStr = null; + + @Argument(shortName="nofilters", fullName="disableFilters", required=false, doc="Disable filters for sites where the phase can't be determined, where the parental origin of the alleles is ambiguous (i.e. everyone is heterozygous), or Mendelian violations") + public Boolean noFilters = false; + + @Output + protected VCFWriter vcfWriter = null; + + private String SAMPLE_NAME_MOM; + private String SAMPLE_NAME_DAD; + private String SAMPLE_NAME_CHILD; + + private final String ROD_NAME = "variant"; + private final String AMBIGUOUS_ALLELE_ORIGIN_FILTER_NAME = "AmbiguousAlleleOrigin"; + private final String INSUFFICIENT_DATA_FILTER_NAME = "InsufficientInformation"; + private final String MENDELIAN_VIOLATION_FILTER_NAME = "MendelianViolation"; + private final String TRANSMISSION_PROBABILITY_TAG_NAME = "TP"; + private final String SOURCE_NAME = "PhaseByTransmission"; + + private final Double MENDELIAN_VIOLATION_PRIOR = 1e-8; + + /** + * Parse the familial relationship specification, and initialize VCF writer + */ + public void initialize() { + String[] pieces = familyStr.split("[\\+\\=]"); + + SAMPLE_NAME_MOM = pieces[0]; + SAMPLE_NAME_DAD = pieces[1]; + SAMPLE_NAME_CHILD = pieces[2]; + + ArrayList rodNames = new ArrayList(); + rodNames.add(ROD_NAME); + + Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); + Set vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); + + if (vcfSamples.size() != 3) { + throw new UserException("File to phase by transmission contains more than three samples. This walker only" + + "accepts VCFs with three samples, so that the meaning of the applied filters is" + + "unambiguous."); + } + + if (!vcfSamples.contains(SAMPLE_NAME_MOM) || !vcfSamples.contains(SAMPLE_NAME_DAD) || !vcfSamples.contains(SAMPLE_NAME_CHILD)) { + throw new UserException("One or more of the samples specified in the familyPattern argument is not present" + + "in this file. Please supply a VCF file that contains only three samples: the" + + "mother, the father, and the child"); + } + + Set samples = new TreeSet(); + samples.add(SAMPLE_NAME_MOM); + samples.add(SAMPLE_NAME_DAD); + samples.add(SAMPLE_NAME_CHILD); + + Set headerLines = new HashSet(); + headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit())); + + if (!noFilters) { + headerLines.add(new VCFFilterHeaderLine(AMBIGUOUS_ALLELE_ORIGIN_FILTER_NAME, "The parental origin of each of the child's allele cannot be determined (ie everyone is heterozygous)")); + headerLines.add(new VCFFilterHeaderLine(INSUFFICIENT_DATA_FILTER_NAME, "The phase of the child's genotype cannot be determined (ie someone is a no-call)")); + headerLines.add(new VCFFilterHeaderLine(MENDELIAN_VIOLATION_FILTER_NAME, "No combination of the parents' alleles can yield the child's genotype (ie a possible Mendelian violation)")); + } + + headerLines.add(new VCFInfoHeaderLine(TRANSMISSION_PROBABILITY_TAG_NAME, 1, VCFHeaderLineType.Float, "Probability that the phase is correct given that the genotypes are correct")); + vcfWriter.writeHeader(new VCFHeader(headerLines, samples)); + } + + private double computeTransmissionLikelihoodOfGenotypeConfiguration(Genotype mom, Genotype dad, Genotype child) { + double[] momLikelihoods = MathUtils.normalizeFromLog10(mom.getLikelihoods().getAsVector()); + double[] dadLikelihoods = MathUtils.normalizeFromLog10(dad.getLikelihoods().getAsVector()); + double[] childLikelihoods = MathUtils.normalizeFromLog10(child.getLikelihoods().getAsVector()); + + int momIndex = mom.getType().ordinal() - 1; + int dadIndex = dad.getType().ordinal() - 1; + int childIndex = child.getType().ordinal() - 1; + + return momLikelihoods[momIndex]*dadLikelihoods[dadIndex]*childLikelihoods[childIndex]; + } + + private ArrayList createAllThreeGenotypes(Allele refAllele, Allele altAllele, Genotype g) { + List homRefAlleles = new ArrayList(); + homRefAlleles.add(refAllele); + homRefAlleles.add(refAllele); + Genotype homRef = new Genotype(g.getSampleName(), homRefAlleles, g.getNegLog10PError(), null, g.getAttributes(), false); + + List hetAlleles = new ArrayList(); + hetAlleles.add(refAllele); + hetAlleles.add(altAllele); + Genotype het = new Genotype(g.getSampleName(), hetAlleles, g.getNegLog10PError(), null, g.getAttributes(), false); + + List homVarAlleles = new ArrayList(); + homVarAlleles.add(altAllele); + homVarAlleles.add(altAllele); + Genotype homVar = new Genotype(g.getSampleName(), homVarAlleles, g.getNegLog10PError(), null, g.getAttributes(), false); + + ArrayList genotypes = new ArrayList(); + genotypes.add(homRef); + genotypes.add(het); + genotypes.add(homVar); + + return genotypes; + } + + private int getNumberOfMatchingAlleles(Allele alleleToMatch, Genotype g) { + List alleles = g.getAlleles(); + int matchingAlleles = 0; + + for (Allele a : alleles) { + if (!alleleToMatch.equals(a)) { + matchingAlleles++; + } + } + + return matchingAlleles; + } + + private boolean isMendelianViolation(Allele refAllele, Allele altAllele, Genotype mom, Genotype dad, Genotype child) { + int numMomRefAlleles = getNumberOfMatchingAlleles(refAllele, mom) > 0 ? 1 : 0; + int numMomAltAlleles = getNumberOfMatchingAlleles(altAllele, mom) > 0 ? 1 : 0; + + int numDadRefAlleles = getNumberOfMatchingAlleles(refAllele, dad) > 0 ? 1 : 0; + int numDadAltAlleles = getNumberOfMatchingAlleles(altAllele, dad) > 0 ? 1 : 0; + + int numChildRefAlleles = getNumberOfMatchingAlleles(refAllele, child); + int numChildAltAlleles = getNumberOfMatchingAlleles(altAllele, child); + + return (numMomRefAlleles + numDadRefAlleles < numChildRefAlleles || numMomAltAlleles + numDadAltAlleles < numChildAltAlleles); + } + + private ArrayList getPhasedGenotypes(Genotype mom, Genotype dad, Genotype child) { + Set possiblePhasedChildGenotypes = new HashSet(); + + for (Allele momAllele : mom.getAlleles()) { + for (Allele dadAllele : dad.getAlleles()) { + ArrayList possiblePhasedChildAlleles = new ArrayList(); + possiblePhasedChildAlleles.add(momAllele); + possiblePhasedChildAlleles.add(dadAllele); + + Genotype possiblePhasedChildGenotype = new Genotype(child.getSampleName(), possiblePhasedChildAlleles, child.getNegLog10PError(), child.getFilters(), child.getAttributes(), true); + + possiblePhasedChildGenotypes.add(possiblePhasedChildGenotype); + } + } + + ArrayList finalGenotypes = new ArrayList(); + + for (Genotype phasedChildGenotype : possiblePhasedChildGenotypes) { + if (child.sameGenotype(phasedChildGenotype, true)) { + Allele momTransmittedAllele = phasedChildGenotype.getAllele(0); + Allele momUntransmittedAllele = mom.getAllele(0) != momTransmittedAllele ? mom.getAllele(0) : mom.getAllele(1); + + ArrayList phasedMomAlleles = new ArrayList(); + phasedMomAlleles.add(momTransmittedAllele); + phasedMomAlleles.add(momUntransmittedAllele); + + Genotype phasedMomGenotype = new Genotype(mom.getSampleName(), phasedMomAlleles, mom.getNegLog10PError(), mom.getFilters(), mom.getAttributes(), true); + + Allele dadTransmittedAllele = phasedChildGenotype.getAllele(1); + Allele dadUntransmittedAllele = dad.getAllele(0) != dadTransmittedAllele ? dad.getAllele(0) : dad.getAllele(1); + + ArrayList phasedDadAlleles = new ArrayList(); + phasedDadAlleles.add(dadTransmittedAllele); + phasedDadAlleles.add(dadUntransmittedAllele); + + Genotype phasedDadGenotype = new Genotype(dad.getSampleName(), phasedDadAlleles, dad.getNegLog10PError(), dad.getFilters(), dad.getAttributes(), true); + + finalGenotypes.add(phasedMomGenotype); + finalGenotypes.add(phasedDadGenotype); + finalGenotypes.add(phasedChildGenotype); + + return finalGenotypes; + } + } + + finalGenotypes.add(mom); + finalGenotypes.add(dad); + finalGenotypes.add(child); + + return finalGenotypes; + } + + private VariantContext phaseTrioGenotypes(VariantContext vc) { + Genotype mom = vc.getGenotype(SAMPLE_NAME_MOM); + Genotype dad = vc.getGenotype(SAMPLE_NAME_DAD); + Genotype child = vc.getGenotype(SAMPLE_NAME_CHILD); + + Set filters = new HashSet(); + filters.addAll(vc.getFilters()); + + Map attributes = new HashMap(); + attributes.putAll(vc.getAttributes()); + attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, 0.0); + + ArrayList finalGenotypes = new ArrayList(); + finalGenotypes.add(mom); + finalGenotypes.add(dad); + finalGenotypes.add(child); + + if (!mom.isCalled() || !dad.isCalled() || !child.isCalled()) { + filters.add(INSUFFICIENT_DATA_FILTER_NAME); + } else { + ArrayList possibleMomGenotypes = createAllThreeGenotypes(vc.getReference(), vc.getAlternateAllele(0), mom); + ArrayList possibleDadGenotypes = createAllThreeGenotypes(vc.getReference(), vc.getAlternateAllele(0), dad); + ArrayList possibleChildGenotypes = createAllThreeGenotypes(vc.getReference(), vc.getAlternateAllele(0), child); + + double bestConfigurationLikelihood = 0.0; + double bestPrior = 0.0; + Genotype bestMomGenotype = mom; + Genotype bestDadGenotype = dad; + Genotype bestChildGenotype = child; + + double norm = 0.0; + + for (Genotype momGenotype : possibleMomGenotypes) { + for (Genotype dadGenotype : possibleDadGenotypes) { + for (Genotype childGenotype : possibleChildGenotypes) { + double prior = isMendelianViolation(vc.getReference(), vc.getAlternateAllele(0), momGenotype, dadGenotype, childGenotype) ? MENDELIAN_VIOLATION_PRIOR : 1.0 - 12*MENDELIAN_VIOLATION_PRIOR; + double configurationLikelihood = computeTransmissionLikelihoodOfGenotypeConfiguration(momGenotype, dadGenotype, childGenotype); + norm += prior*configurationLikelihood; + + if (prior*configurationLikelihood > bestPrior*bestConfigurationLikelihood) { + bestConfigurationLikelihood = configurationLikelihood; + bestPrior = prior; + bestMomGenotype = momGenotype; + bestDadGenotype = dadGenotype; + bestChildGenotype = childGenotype; + } + } + } + } + + if (isMendelianViolation(vc.getReference(), vc.getAlternateAllele(0), bestMomGenotype, bestDadGenotype, bestChildGenotype)) { + filters.add(MENDELIAN_VIOLATION_FILTER_NAME); + } else if (bestMomGenotype.isHet() && bestDadGenotype.isHet() && bestChildGenotype.isHet()) { + filters.add(AMBIGUOUS_ALLELE_ORIGIN_FILTER_NAME); + } else { + finalGenotypes = getPhasedGenotypes(bestMomGenotype, bestDadGenotype, bestChildGenotype); + + attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm); + } + } + + return new VariantContext(SOURCE_NAME, vc.getChr(), vc.getStart(), vc.getStart(), vc.getAlleles(), finalGenotypes, vc.getNegLog10PError(), noFilters ? vc.getFilters() : filters, attributes); + } + + /** + * For each variant in the file, determine the phasing for the child and replace the child's genotype with the trio's genotype + * + * @param tracker the reference meta-data tracker + * @param ref the reference context + * @param context the alignment context + * @return null + */ + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (tracker != null) { + Collection vcs = tracker.getVariantContexts(ref, ROD_NAME, null, context.getLocation(), true, true); + + for (VariantContext vc : vcs) { + vcfWriter.add(phaseTrioGenotypes(vc), ref.getBase()); + } + } + + return null; + } + + /** + * Provide an initial value for reduce computations. + * + * @return Initial value of reduce. + */ + @Override + public Integer reduceInit() { + return null; + } + + /** + * Reduces a single map with the accumulator provided as the ReduceType. + * + * @param value result of the map. + * @param sum accumulator for the reduce. + * @return accumulator with result of the map taken into account. + */ + @Override + public Integer reduce(Integer value, Integer sum) { + return null; + } +} From 9992c373be8bda5fd4e5999ac3cac36c35e9bb96 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 17 Jul 2011 20:29:58 -0400 Subject: [PATCH 32/39] Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. --- .../analyzecovariates/AnalyzeCovariates.java | 11 +++-- .../sting/commandline/Argument.java | 7 +-- .../commandline/ArgumentDefinitionGroup.java | 4 +- .../commandline/ArgumentDefinitions.java | 4 +- .../commandline/ArgumentTypeDescriptor.java | 6 +-- .../sting/commandline/CommandLineProgram.java | 10 +++- .../sting/commandline/CommandLineUtils.java | 10 +++- .../MissingArgumentValueException.java | 2 - .../sting/commandline/ParsingEngine.java | 10 ++-- .../sting/commandline/ParsingMethod.java | 4 +- .../sting/gatk/CommandLineExecutable.java | 21 +++------ .../sting/gatk/CommandLineGATK.java | 10 ++-- .../sting/gatk/GenomeAnalysisEngine.java | 15 ++---- .../sting/gatk/ReadMetrics.java | 9 ++-- .../sting/gatk/ReadProperties.java | 1 - .../sting/gatk/WalkerManager.java | 7 ++- .../arguments/GATKArgumentCollection.java | 11 ++--- .../sting/gatk/contexts/AlignmentContext.java | 6 +-- .../gatk/contexts/AlignmentContextUtils.java | 2 +- .../sting/gatk/contexts/ReferenceContext.java | 9 ++-- .../datasources/providers/AllLocusView.java | 16 +++---- .../providers/LocusReferenceView.java | 11 ++--- .../providers/LocusShardDataProvider.java | 9 ++-- .../gatk/datasources/providers/LocusView.java | 2 +- .../ManagingReferenceOrderedView.java | 2 +- .../providers/ReadReferenceView.java | 3 +- .../providers/ReadShardDataProvider.java | 7 ++- .../gatk/datasources/providers/ReadView.java | 5 +- .../datasources/providers/ReferenceView.java | 18 ++++---- .../datasources/providers/RodLocusView.java | 4 +- .../providers/ShardDataProvider.java | 5 +- .../reads/BAMBlockStartIterator.java | 5 -- .../gatk/datasources/reads/BAMSchedule.java | 7 +-- .../gatk/datasources/reads/BAMScheduler.java | 12 +---- .../gatk/datasources/reads/FilePointer.java | 10 +--- .../gatk/datasources/reads/GATKBAMIndex.java | 14 ++---- .../datasources/reads/GATKBAMIndexData.java | 6 +-- .../datasources/reads/IntervalSharder.java | 11 +---- .../gatk/datasources/reads/LocusShard.java | 3 +- .../datasources/reads/LocusShardStrategy.java | 17 +++---- .../datasources/reads/MonolithicShard.java | 2 +- .../reads/MonolithicShardStrategy.java | 2 +- .../gatk/datasources/reads/ReadShard.java | 14 +++--- .../datasources/reads/ReadShardStrategy.java | 5 +- .../gatk/datasources/reads/SAMDataSource.java | 14 +++--- .../sting/gatk/datasources/reads/Shard.java | 8 +--- .../reads/ShardStrategyFactory.java | 4 +- .../reads/utilities/BAMFileStat.java | 8 ++-- .../reads/utilities/BAMTagRenamer.java | 8 ++-- .../reads/utilities/PrintBGZFBounds.java | 1 - .../reference/ReferenceDataSource.java | 11 ++--- .../gatk/datasources/rmd/ResourcePool.java | 6 +-- .../datasources/sample/SampleDataSource.java | 5 +- .../sting/gatk/examples/CoverageBySample.java | 17 ++++--- .../gatk/examples/GATKPaperGenotyper.java | 4 +- .../sting/gatk/executive/Accumulator.java | 12 ++--- .../executive/HierarchicalMicroScheduler.java | 18 ++++---- .../gatk/executive/LinearMicroScheduler.java | 11 ++--- .../sting/gatk/executive/MicroScheduler.java | 25 +++++----- .../sting/gatk/executive/OutputMergeTask.java | 3 +- .../sting/gatk/executive/ReduceTree.java | 4 +- .../sting/gatk/executive/ShardTraverser.java | 6 +-- .../sting/gatk/executive/TreeReducer.java | 2 +- .../sting/gatk/executive/WindowMaker.java | 19 ++++---- .../sting/gatk/filters/BadCigarFilter.java | 6 ++- .../sting/gatk/filters/BadMateFilter.java | 1 - .../filters/CountingFilteringIterator.java | 13 +++--- .../gatk/filters/DuplicateReadFilter.java | 1 - .../FailsVendorQualityCheckReadFilter.java | 1 - .../sting/gatk/filters/FilterManager.java | 3 -- .../gatk/filters/MalformedReadFilter.java | 2 +- .../filters/MappingQualityReadFilter.java | 1 - .../MappingQualityUnavailableReadFilter.java | 1 - .../gatk/filters/MaxInsertSizeFilter.java | 1 - .../gatk/filters/MaxReadLengthFilter.java | 1 - .../gatk/filters/MissingReadGroupFilter.java | 1 - .../NoOriginalQualityScoresFilter.java | 1 - .../NotPrimaryAlignmentReadFilter.java | 1 - .../sting/gatk/filters/Platform454Filter.java | 2 - .../sting/gatk/filters/PlatformFilter.java | 4 +- .../gatk/filters/PlatformUnitFilter.java | 10 ++-- .../sting/gatk/filters/ReadFilter.java | 1 - .../filters/ReadGroupBlackListFilter.java | 13 +++--- .../sting/gatk/filters/ReadStrandFilter.java | 1 - .../sting/gatk/filters/SampleFilter.java | 3 +- .../gatk/filters/SingleReadGroupFilter.java | 3 +- .../gatk/filters/UnmappedReadFilter.java | 1 - .../sting/gatk/io/DirectOutputTracker.java | 4 +- .../sting/gatk/io/OutputTracker.java | 16 +++---- .../sting/gatk/io/StingSAMFileWriter.java | 2 +- .../gatk/io/ThreadLocalOutputTracker.java | 9 ++-- .../gatk/io/storage/OutputStreamStorage.java | 4 +- .../gatk/io/storage/SAMFileWriterStorage.java | 9 ++-- .../sting/gatk/io/storage/StorageFactory.java | 2 +- .../gatk/io/storage/VCFWriterStorage.java | 19 +++++--- .../OutputStreamArgumentTypeDescriptor.java | 2 +- .../sting/gatk/io/stubs/OutputStreamStub.java | 4 +- .../SAMFileReaderArgumentTypeDescriptor.java | 8 ++-- .../SAMFileWriterArgumentTypeDescriptor.java | 9 ++-- .../gatk/io/stubs/SAMFileWriterStub.java | 15 +++--- .../VCFWriterArgumentTypeDescriptor.java | 7 ++- .../sting/gatk/io/stubs/VCFWriterStub.java | 18 ++++---- .../gatk/iterators/BoundedReadIterator.java | 4 +- .../gatk/iterators/BufferingReadIterator.java | 5 +- .../gatk/iterators/DownsampleIterator.java | 3 +- .../gatk/iterators/GenomeLocusIterator.java | 2 +- .../sting/gatk/iterators/LocusIterator.java | 3 +- .../gatk/iterators/LocusIteratorByState.java | 20 +++++--- .../sting/gatk/iterators/NullSAMIterator.java | 1 - .../iterators/PositionTrackingIterator.java | 1 - .../iterators/ReadFormattingIterator.java | 7 +-- .../gatk/iterators/StingSAMIterator.java | 1 - .../sting/gatk/phonehome/GATKRunReport.java | 5 +- .../sting/gatk/refdata/RODRecordIterator.java | 10 ++-- .../sting/gatk/refdata/RODRecordListImpl.java | 2 +- .../gatk/refdata/RefMetaDataTracker.java | 4 +- .../gatk/refdata/SeekableRODIterator.java | 2 +- .../gatk/refdata/VariantContextAdaptors.java | 12 ++--- .../annotator/AnnotatorInputTableCodec.java | 12 ++--- .../annotator/AnnotatorInputTableFeature.java | 4 +- .../refdata/features/beagle/BeagleCodec.java | 10 ++-- .../features/beagle/BeagleFeature.java | 5 +- .../features/refseq/RefSeqFeature.java | 3 +- .../features/sampileup/SAMPileupCodec.java | 4 +- .../features/sampileup/SAMPileupFeature.java | 3 +- .../features/samread/SAMReadCodec.java | 6 +-- .../refdata/features/table/BedTableCodec.java | 5 -- .../refdata/features/table/TableCodec.java | 6 +-- .../refdata/features/table/TableFeature.java | 2 +- .../gatk/refdata/indexer/RMDIndexer.java | 1 - .../gatk/refdata/tracks/QueryableTrack.java | 1 - .../sting/gatk/refdata/tracks/RMDTrack.java | 2 - .../tracks/builders/RMDTrackBuilder.java | 8 ++-- .../utils/FeatureToGATKFeatureIterator.java | 2 - .../sting/gatk/refdata/utils/GATKFeature.java | 2 - .../LocationAwareSeekableRODIterator.java | 4 -- .../StringToGenomeLocIteratorAdapter.java | 2 +- .../refdata/utils/helpers/DbSNPHelper.java | 2 +- .../gatk/traversals/TraversalEngine.java | 9 ++-- .../gatk/traversals/TraverseDuplicates.java | 3 +- .../sting/gatk/traversals/TraverseLoci.java | 1 - .../gatk/traversals/TraverseReadPairs.java | 16 ++++--- .../sting/gatk/traversals/TraverseReads.java | 8 ++-- .../sting/gatk/walkers/Allows.java | 7 +-- .../sting/gatk/walkers/BAQMode.java | 7 +-- .../broadinstitute/sting/gatk/walkers/By.java | 7 +-- .../sting/gatk/walkers/ClipReadsWalker.java | 26 +++++------ .../sting/gatk/walkers/DuplicateWalker.java | 7 +-- .../walkers/FindReadsWithNamesWalker.java | 1 - .../sting/gatk/walkers/FlagStatWalker.java | 6 +-- .../walkers/GCContentByIntervalWalker.java | 3 +- .../sting/gatk/walkers/LocusWalker.java | 7 ++- .../sting/gatk/walkers/PileupWalker.java | 8 ++-- .../sting/gatk/walkers/PrintRODsWalker.java | 4 +- .../sting/gatk/walkers/PrintReadsWalker.java | 6 +-- .../sting/gatk/walkers/ReadWalker.java | 2 +- .../sting/gatk/walkers/Requires.java | 7 +-- .../gatk/walkers/SplitSamFileWalker.java | 18 +++++--- .../sting/gatk/walkers/Walker.java | 6 +-- .../sting/gatk/walkers/WalkerName.java | 6 +-- .../sting/gatk/walkers/Window.java | 5 +- .../gatk/walkers/annotator/AlleleBalance.java | 16 +++---- .../annotator/AlleleBalanceBySample.java | 14 ++++-- .../walkers/annotator/AnnotationByDepth.java | 3 +- .../gatk/walkers/annotator/BaseCounts.java | 12 ++--- .../annotator/BaseQualityRankSumTest.java | 8 ++-- .../walkers/annotator/ChromosomeCounts.java | 20 ++++---- .../walkers/annotator/DepthOfCoverage.java | 15 +++--- .../annotator/DepthPerAlleleBySample.java | 19 ++++---- .../gatk/walkers/annotator/FisherStrand.java | 14 +++--- .../gatk/walkers/annotator/GCContent.java | 13 +++--- .../sting/gatk/walkers/annotator/GLstats.java | 15 +++--- .../walkers/annotator/HaplotypeScore.java | 32 +++++++------ .../gatk/walkers/annotator/HardyWeinberg.java | 15 +++--- .../walkers/annotator/HomopolymerRun.java | 10 ++-- .../gatk/walkers/annotator/IndelType.java | 6 +-- .../sting/gatk/walkers/annotator/LowMQ.java | 12 ++--- .../annotator/MappingQualityRankSumTest.java | 8 ++-- .../walkers/annotator/MappingQualityZero.java | 8 ++-- .../annotator/MappingQualityZeroBySample.java | 20 ++++---- .../annotator/MappingQualityZeroFraction.java | 6 +-- .../gatk/walkers/annotator/NBaseCount.java | 6 +-- .../gatk/walkers/annotator/QualByDepth.java | 12 ++--- .../walkers/annotator/RMSMappingQuality.java | 15 +++--- .../gatk/walkers/annotator/RankSumTest.java | 15 +++--- .../ReadDepthAndAllelicFractionBySample.java | 21 ++++----- .../walkers/annotator/ReadPosRankSumTest.java | 11 +++-- .../gatk/walkers/annotator/SBByDepth.java | 10 ++-- .../gatk/walkers/annotator/SampleList.java | 10 ++-- .../walkers/annotator/SpanningDeletions.java | 6 +-- .../annotator/TechnologyComposition.java | 6 ++- .../walkers/annotator/VariantAnnotator.java | 13 +++--- .../annotator/VariantAnnotatorEngine.java | 31 ++++++------- .../genomicannotator/GenomicAnnotation.java | 14 +++--- .../genomicannotator/GenomicAnnotator.java | 22 ++++----- .../annotator/genomicannotator/JoinTable.java | 6 +-- .../genomicannotator/JoinTableParser.java | 8 ++-- .../TranscriptToGenomicInfo.java | 15 ++---- .../interfaces/GenotypeAnnotation.java | 10 ++-- .../interfaces/InfoFieldAnnotation.java | 8 ++-- .../beagle/BeagleOutputToVCFWalker.java | 14 +++--- .../beagle/ProduceBeagleInputWalker.java | 13 +++--- .../VariantsToBeagleUnphasedWalker.java | 19 ++++---- .../walkers/coverage/CallableLociWalker.java | 6 +-- .../coverage/CoarseCoverageWalker.java | 7 ++- .../coverage/CompareCallableLociWalker.java | 10 ++-- .../gatk/walkers/coverage/CoverageUtils.java | 4 +- .../coverage/DepthOfCoverageWalker.java | 11 +++-- .../walkers/diffengine/BAMDiffableReader.java | 13 ++---- .../gatk/walkers/diffengine/DiffElement.java | 4 +- .../gatk/walkers/diffengine/DiffValue.java | 2 - .../walkers/diffengine/VCFDiffableReader.java | 5 +- .../fasta/FastaAlternateReferenceWalker.java | 2 +- .../walkers/fasta/FastaReferenceWalker.java | 5 +- .../gatk/walkers/filters/ClusteredSnps.java | 2 +- .../walkers/filters/FiltrationContext.java | 2 +- .../filters/FiltrationContextWindow.java | 4 +- .../filters/VariantFiltrationWalker.java | 13 +++--- .../AlleleFrequencyCalculationModel.java | 7 +-- .../genotyper/DiploidIndelGenotypePriors.java | 2 - .../DiploidSNPGenotypeLikelihoods.java | 11 +++-- .../genotyper/ExactAFCalculationModel.java | 15 ++++-- .../GenotypeLikelihoodsCalculationModel.java | 2 +- .../genotyper/GridSearchAFEstimation.java | 10 ++-- ...elGenotypeLikelihoodsCalculationModel.java | 11 ++--- .../MultiallelicGenotypeLikelihoods.java | 2 +- ...NPGenotypeLikelihoodsCalculationModel.java | 18 ++++---- .../walkers/genotyper/UGCalcLikelihoods.java | 8 ++-- .../walkers/genotyper/UGCallVariants.java | 8 ++-- .../genotyper/UnifiedArgumentCollection.java | 1 - .../walkers/genotyper/UnifiedGenotyper.java | 19 ++++---- .../genotyper/UnifiedGenotyperEngine.java | 16 ++++--- .../indels/ConstrainedMateFixingManager.java | 6 ++- .../indels/HaplotypeIndelErrorModel.java | 7 +-- .../gatk/walkers/indels/IndelRealigner.java | 38 +++++++-------- .../gatk/walkers/indels/LeftAlignIndels.java | 6 ++- .../indels/PairHMMIndelErrorModel.java | 27 +++++------ .../walkers/indels/RealignedReadCounter.java | 24 ++++++---- .../indels/RealignerTargetCreator.java | 12 ++--- ...CoordinateComparatorWithUnmappedReads.java | 3 +- .../indels/SomaticIndelDetectorWalker.java | 46 +++++++++++-------- .../gatk/walkers/phasing/AllelePair.java | 2 +- .../walkers/phasing/AnnotateMNPsWalker.java | 9 ++-- .../gatk/walkers/phasing/MergeMNPsWalker.java | 8 ++-- ...eSegregatingAlternateAllelesVCFWriter.java | 15 +++--- ...ergeSegregatingAlternateAllelesWalker.java | 10 ++-- .../phasing/ReadBackedPhasingWalker.java | 21 +++++---- .../gatk/walkers/phasing/SNPallelePair.java | 4 +- .../sting/gatk/walkers/phasing/WriteVCF.java | 2 +- .../sting/gatk/walkers/qc/CountIntervals.java | 4 +- .../gatk/walkers/qc/CountLociWalker.java | 1 - .../gatk/walkers/qc/CountPairsWalker.java | 6 +-- .../gatk/walkers/qc/CountReadsWalker.java | 4 +- .../gatk/walkers/qc/CountRodByRefWalker.java | 2 +- .../sting/gatk/walkers/qc/CountRodWalker.java | 11 +++-- .../gatk/walkers/qc/CycleQualityWalker.java | 24 +++++----- .../walkers/qc/PrintLocusContextWalker.java | 12 ++--- .../walkers/qc/ReadClippingStatsWalker.java | 27 ++++++----- .../gatk/walkers/qc/ReadValidationWalker.java | 8 ++-- .../walkers/qc/RodSystemValidationWalker.java | 6 ++- .../walkers/qc/ValidatingPileupWalker.java | 8 ++-- .../CountCovariatesGatherer.java | 1 - .../recalibration/CountCovariatesWalker.java | 13 +++--- .../walkers/recalibration/CycleCovariate.java | 1 - .../walkers/recalibration/DinucCovariate.java | 5 +- .../recalibration/RecalDataManager.java | 18 ++++---- .../recalibration/RecalDatumOptimized.java | 2 +- .../TableRecalibrationWalker.java | 30 ++++++------ .../walkers/sequenom/CreateSequenomMask.java | 4 +- .../walkers/sequenom/PickSequenomProbes.java | 18 ++++---- .../varianteval/VariantEvalWalker.java | 17 +++---- .../evaluators/CompEvalGenotypes.java | 2 +- .../varianteval/evaluators/CompOverlap.java | 6 +-- .../varianteval/evaluators/CountVariants.java | 8 ++-- .../evaluators/GenotypeConcordance.java | 12 ++--- .../evaluators/GenotypePhasingEvaluator.java | 7 +-- .../evaluators/IndelLengthHistogram.java | 8 ++-- .../evaluators/IndelMetricsByAC.java | 6 +-- .../evaluators/IndelStatistics.java | 8 ++-- .../MendelianViolationEvaluator.java | 8 ++-- .../evaluators/PrintMissingComp.java | 6 +-- .../evaluators/SamplePreviousGenotypes.java | 2 +- .../evaluators/SimpleMetricsByAC.java | 7 +-- .../evaluators/ThetaVariantEvaluator.java | 6 +-- .../evaluators/TiTvVariantEvaluator.java | 8 ++-- .../evaluators/ValidationReport.java | 12 ++--- .../evaluators/VariantEvaluator.java | 2 +- .../evaluators/VariantQualityScore.java | 10 ++-- .../stratifications/AlleleCount.java | 5 +- .../stratifications/AlleleFrequency.java | 2 +- .../varianteval/stratifications/CompRod.java | 2 +- .../varianteval/stratifications/Contig.java | 2 +- .../varianteval/stratifications/CpG.java | 2 +- .../stratifications/Degeneracy.java | 4 +- .../varianteval/stratifications/EvalRod.java | 2 +- .../varianteval/stratifications/Filter.java | 2 +- .../stratifications/FunctionalClass.java | 2 +- .../stratifications/JexlExpression.java | 4 +- .../varianteval/stratifications/Novelty.java | 2 +- .../varianteval/stratifications/Sample.java | 2 +- .../stratifications/VariantStratifier.java | 3 +- .../util/NewEvaluationContext.java | 2 +- .../util/SortableJexlVCMatchExp.java | 2 +- .../varianteval/util/VariantEvalUtils.java | 4 +- .../ApplyRecalibration.java | 12 ++--- .../walkers/variantrecalibration/Tranche.java | 7 ++- .../VQSRCalibrationCurve.java | 2 +- .../VariantDataManager.java | 6 ++- .../VariantRecalibrator.java | 4 +- .../walkers/variantutils/CombineVariants.java | 13 +++--- .../variantutils/FilterLiftedVariants.java | 19 ++++---- .../variantutils/LeftAlignVariants.java | 12 ++--- .../variantutils/LiftoverVariants.java | 32 ++++++------- .../variantutils/RandomlySplitVariants.java | 13 +++--- .../walkers/variantutils/SelectVariants.java | 19 ++++---- .../variantutils/ValidateVariants.java | 21 +++++---- .../VariantValidationAssessor.java | 13 +++--- .../walkers/variantutils/VariantsToTable.java | 5 +- .../walkers/variantutils/VariantsToVCF.java | 24 +++++----- .../sting/jna/clibrary/LibC.java | 5 +- .../sting/jna/lsf/v7_0_6/LibLsf.java | 2 +- .../gatk/ArgumentDefinitionField.java | 7 ++- .../queue/extensions/gatk/ArgumentField.java | 5 +- .../gatk/GATKExtensionsGenerator.java | 7 ++- .../sting/utils/DisjointSet.java | 4 +- .../broadinstitute/sting/utils/GenomeLoc.java | 1 - .../sting/utils/GenomeLocParser.java | 6 ++- .../sting/utils/IndelUtils.java | 2 +- .../broadinstitute/sting/utils/MathUtils.java | 9 ++-- .../sting/utils/MendelianViolation.java | 7 +-- .../broadinstitute/sting/utils/PathUtils.java | 4 +- .../sting/utils/ReservoirDownsampler.java | 4 +- .../sting/utils/SWPairwiseAlignment.java | 7 ++- .../sting/utils/SampleUtils.java | 6 +-- .../sting/utils/SimpleTimer.java | 5 +- .../org/broadinstitute/sting/utils/Utils.java | 5 +- .../broadinstitute/sting/utils/baq/BAQ.java | 6 +-- .../sting/utils/baq/BAQSamIterator.java | 5 +- .../sting/utils/bed/BedParser.java | 5 +- .../sting/utils/classloader/JVMUtils.java | 2 +- .../sting/utils/clipreads/ClippingOp.java | 3 -- .../sting/utils/clipreads/ReadClipper.java | 1 - .../codecs/completegenomics/CGVarCodec.java | 1 - .../utils/codecs/soapsnp/SoapSNPCodec.java | 6 +-- .../utils/codecs/vcf/StandardVCFWriter.java | 4 +- .../sting/utils/codecs/vcf/VCFParser.java | 4 +- .../sting/utils/codecs/vcf/VCFUtils.java | 4 +- .../utils/collections/NestedHashMap.java | 3 +- .../utils/collections/RODMergingIterator.java | 7 ++- .../sting/utils/duplicates/DupUtils.java | 9 ++-- .../sting/utils/exceptions/UserException.java | 3 +- .../CachingIndexedFastaSequenceFile.java | 7 +-- .../sting/utils/genotype/DiploidGenotype.java | 1 - .../sting/utils/genotype/Haplotype.java | 8 ++-- .../sting/utils/help/ApplicationDetails.java | 8 ++-- .../sting/utils/help/DescriptionTaglet.java | 1 - .../sting/utils/help/DisplayNameTaglet.java | 1 - .../sting/utils/help/HelpFormatter.java | 12 ++--- .../sting/utils/help/HelpTaglet.java | 4 +- .../help/ResourceBundleExtractorDoclet.java | 14 +++--- .../sting/utils/help/SummaryTaglet.java | 1 - .../sting/utils/instrumentation/Sizeof.java | 2 +- .../interval/IntervalFileMergingIterator.java | 6 +-- .../sting/utils/interval/IntervalUtils.java | 4 +- .../interval/NwayIntervalMergingIterator.java | 3 +- .../interval/OverlappingIntervalIterator.java | 3 +- .../pileup/AbstractReadBackedPileup.java | 11 ++--- .../pileup/ExtendedEventPileupElement.java | 3 -- .../sting/utils/pileup/FragmentPileup.java | 5 +- .../pileup/MergingPileupElementIterator.java | 2 +- .../sting/utils/pileup/PileupElement.java | 5 +- .../pileup/ReadBackedExtendedEventPileup.java | 6 +-- .../ReadBackedExtendedEventPileupImpl.java | 5 +- .../sting/utils/pileup/ReadBackedPileup.java | 5 +- .../utils/pileup/ReadBackedPileupImpl.java | 2 +- .../sting/utils/sam/AlignmentUtils.java | 9 ++-- .../utils/sam/ArtificialReadsTraversal.java | 16 +++---- .../utils/sam/ArtificialSAMFileReader.java | 16 ++++--- .../utils/sam/ArtificialSAMIterator.java | 5 +- .../utils/sam/ArtificialSAMQueryIterator.java | 5 +- .../sting/utils/sam/ComparableSAMRecord.java | 2 - .../utils/sam/GATKSAMReadGroupRecord.java | 2 +- .../sting/utils/sam/GATKSAMRecord.java | 8 ++-- .../sting/utils/sam/ReadUtils.java | 5 +- .../sting/utils/sam/SAMFileReaderBuilder.java | 3 +- .../utils/sam/SimplifyingSAMFileWriter.java | 7 --- .../sting/utils/text/ListFileUtils.java | 1 - .../sting/utils/text/TextFormattingUtils.java | 8 ++-- .../sting/utils/text/XReadLines.java | 6 +-- .../FileBackedGenomeLocProcessingTracker.java | 4 -- .../NoOpGenomeLocProcessingTracker.java | 4 -- .../sting/utils/threading/SharedFileLock.java | 3 -- .../threading/SharedFileThreadSafeLock.java | 5 -- .../sting/utils/variantcontext/Allele.java | 4 +- .../variantcontext/GenotypeLikelihoods.java | 2 +- .../variantcontext/MutableVariantContext.java | 5 +- .../utils/variantcontext/VariantContext.java | 2 +- .../variantcontext/VariantContextUtils.java | 19 +++++--- .../variantcontext/VariantJEXLContext.java | 5 +- .../sting/utils/wiggle/WiggleWriter.java | 2 +- 400 files changed, 1480 insertions(+), 1602 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java index f8e298d88..b9e380295 100755 --- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java +++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java @@ -25,20 +25,21 @@ package org.broadinstitute.sting.analyzecovariates; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.gatk.walkers.recalibration.*; +import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate; +import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum; +import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.commandline.Argument; +import java.io.*; import java.util.ArrayList; import java.util.Collection; -import java.util.List; import java.util.Map; import java.util.regex.Pattern; -import java.io.*; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/commandline/Argument.java b/public/java/src/org/broadinstitute/sting/commandline/Argument.java index b2ee9d1fc..33592287d 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/Argument.java +++ b/public/java/src/org/broadinstitute/sting/commandline/Argument.java @@ -25,12 +25,7 @@ package org.broadinstitute.sting.commandline; -import java.lang.annotation.Documented; -import java.lang.annotation.ElementType; -import java.lang.annotation.Inherited; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; +import java.lang.annotation.*; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java index c36a8e04f..b47677b08 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java @@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.List; -import java.util.Collections; import java.util.ArrayList; +import java.util.Collections; import java.util.Iterator; +import java.util.List; /** * A group of argument definitions. diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java index 39e698ca3..9f92df6e0 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java @@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.Set; -import java.util.HashSet; import java.util.Collection; +import java.util.HashSet; import java.util.Iterator; +import java.util.Set; /** * A collection of argument definitions. diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index 6c50e1784..9c33e084d 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.classloader.JVMUtils; +import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.walkers.Multiplex; import org.broadinstitute.sting.gatk.walkers.Multiplexer; -import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.lang.annotation.Annotation; diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java index d404a2b6e..aba4fc109 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java +++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java @@ -25,14 +25,20 @@ package org.broadinstitute.sting.commandline; -import org.apache.log4j.*; +import org.apache.log4j.FileAppender; +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.apache.log4j.PatternLayout; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.help.ApplicationDetails; import org.broadinstitute.sting.utils.help.HelpFormatter; import java.io.IOException; -import java.util.*; +import java.util.Collection; +import java.util.Collections; +import java.util.EnumSet; +import java.util.Locale; public abstract class CommandLineProgram { diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java index 99608f167..bd2006388 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java +++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java @@ -25,11 +25,17 @@ package org.broadinstitute.sting.commandline; -import org.apache.log4j.*; +import org.apache.log4j.Appender; +import org.apache.log4j.ConsoleAppender; +import org.apache.log4j.Logger; +import org.apache.log4j.PatternLayout; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.*; import java.lang.annotation.Annotation; +import java.util.Collections; +import java.util.Enumeration; +import java.util.LinkedHashMap; +import java.util.Map; /** * Static utility methods for working with command-line arguments. diff --git a/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java b/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java index 8029db7b3..4e6c3a16f 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java +++ b/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java @@ -26,8 +26,6 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.utils.Utils; -import java.util.Collection; - /** * Specifies that a value was missing when attempting to populate an argument. */ diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java index 717c5c522..8423bb2f2 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java @@ -25,16 +25,16 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.classloader.JVMUtils; +import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.classloader.JVMUtils; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.ApplicationDetails; import org.broadinstitute.sting.utils.help.HelpFormatter; -import org.apache.log4j.Logger; -import java.lang.reflect.*; +import java.lang.reflect.Field; import java.util.*; /** diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java index d1cda3ed9..a070cb5a1 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java @@ -27,10 +27,8 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.utils.Utils; -import java.util.regex.Pattern; import java.util.regex.Matcher; -import java.util.List; -import java.util.ArrayList; +import java.util.regex.Pattern; /** * Holds a pattern, along with how to get to the argument definitions that could match that pattern. diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java index fd7e749c3..a080ab439 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java @@ -25,30 +25,21 @@ package org.broadinstitute.sting.gatk; -import org.broadinstitute.sting.commandline.Tags; -import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; -import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor; -import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; +import org.broadinstitute.sting.commandline.CommandLineProgram; +import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType; -import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.Walker; - -import java.io.File; -import java.io.FileNotFoundException; -import java.util.*; - -import net.sf.picard.filter.SamRecordFilter; -import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.ListFileUtils; -import org.broadinstitute.sting.utils.text.XReadLines; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; /** * @author aaron diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 7982f61e2..da2be74bf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -26,13 +26,15 @@ package org.broadinstitute.sting.gatk; import org.broad.tribble.TribbleException; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.ArgumentCollection; +import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.walkers.Attribution; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.text.TextFormattingUtils; -import org.broadinstitute.sting.utils.help.ApplicationDetails; -import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.ApplicationDetails; +import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index f8527c33b..918bc1251 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -28,24 +28,14 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.samtools.*; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.ArgumentException; -import org.broadinstitute.sting.commandline.ArgumentSource; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.commandline.CommandLineUtils; -import org.broadinstitute.sting.commandline.ParsingEngine; -import org.broadinstitute.sting.commandline.Tags; +import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; +import org.broadinstitute.sting.gatk.datasources.reads.*; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.MonolithicShardStrategy; -import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy; -import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategyFactory; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.executive.MicroScheduler; import org.broadinstitute.sting.gatk.filters.FilterManager; import org.broadinstitute.sting.gatk.filters.ReadFilter; @@ -65,6 +55,7 @@ import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java b/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java index 27a86ab3f..7cb615f7f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java +++ b/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java @@ -25,13 +25,12 @@ package org.broadinstitute.sting.gatk; import net.sf.picard.filter.SamRecordFilter; - -import java.util.Map; -import java.util.HashMap; -import java.util.Collections; - import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import java.util.Collections; +import java.util.HashMap; +import java.util.Map; + /** * Holds a bunch of basic information about the traversal. */ diff --git a/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java b/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java index 1a361029a..93fa2d146 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java +++ b/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk; -import net.sf.picard.filter.SamRecordFilter; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileReader; diff --git a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java index 9553f651e..cf190835e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java @@ -25,19 +25,18 @@ package org.broadinstitute.sting.gatk; -import net.sf.picard.filter.SamRecordFilter; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.filters.FilterManager; import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.text.TextFormattingUtils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.help.DescriptionTaglet; import org.broadinstitute.sting.utils.help.DisplayNameTaglet; import org.broadinstitute.sting.utils.help.SummaryTaglet; -import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 93638f21d..ee2e85025 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -26,17 +26,16 @@ package org.broadinstitute.sting.gatk.arguments; import net.sf.samtools.SAMFileReader; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.DownsamplingMethod; -import org.broadinstitute.sting.utils.interval.IntervalSetRule; +import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.interval.IntervalMergingRule; +import org.broadinstitute.sting.utils.interval.IntervalSetRule; import org.simpleframework.xml.*; import org.simpleframework.xml.core.Persister; import org.simpleframework.xml.stream.Format; diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java index 337c2664c..17e4a0743 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java @@ -26,13 +26,13 @@ package org.broadinstitute.sting.gatk.contexts; import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import java.util.*; +import java.util.List; /** * Useful class for forwarding on locusContext data from this iterator diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java index 6a0d30837..1f9a7d705 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.contexts; import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.datasources.sample.Sample; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java index 760b3a7bc..376064cdb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java @@ -25,11 +25,12 @@ package org.broadinstitute.sting.gatk.contexts; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.BaseUtils; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; import net.sf.samtools.util.StringUtil; -import com.google.java.contract.*; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; /** * The section of the reference that overlaps with the given diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java index b36c59a2c..e92599494 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java @@ -1,16 +1,14 @@ package org.broadinstitute.sting.gatk.datasources.providers; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; + +import java.util.Collections; import java.util.List; import java.util.NoSuchElementException; -import java.util.ArrayList; -import java.util.Collections; - -import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.utils.GenomeLoc; -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; /** * User: hanna * Date: May 13, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java index 330a9e4f7..ff312bcac 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -1,13 +1,12 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; +import net.sf.picard.reference.ReferenceSequence; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.sting.gatk.walkers.Reference; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import net.sf.picard.reference.ReferenceSequence; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /* * Copyright (c) 2009 The Broad Institute * diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java index 72b962522..55304da34 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java @@ -1,16 +1,15 @@ package org.broadinstitute.sting.gatk.datasources.providers; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.iterators.LocusIterator; -import org.broadinstitute.sting.gatk.ReadProperties; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; import java.util.Collection; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.GenomeLocParser; - /** * Presents data sharded by locus to the traversal engine. * diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java index b467a2ab5..f9ed0cb74 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.DownsampleType; +import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.iterators.LocusIterator; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java index a91e169c1..223659a46 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java @@ -5,10 +5,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.utils.GenomeLoc; -import java.util.List; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; +import java.util.List; /** * User: hanna * Date: May 21, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java index d2c097f5d..3d62faf49 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java @@ -1,9 +1,8 @@ package org.broadinstitute.sting.gatk.datasources.providers; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.utils.GenomeLoc; /* * Copyright (c) 2009 The Broad Institute * diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java index 5a672b09f..7843e7518 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java @@ -1,14 +1,13 @@ package org.broadinstitute.sting.gatk.datasources.providers; +import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.sting.utils.GenomeLocParser; import java.util.Collection; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.GenomeLocParser; - /** * Present data sharded by read to a traversal engine. * diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java index 0c4b78a7c..e809092d4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java @@ -1,11 +1,10 @@ package org.broadinstitute.sting.gatk.datasources.providers; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import java.util.Collection; import java.util.Arrays; - -import net.sf.samtools.SAMRecord; +import java.util.Collection; /** * User: hanna * Date: May 22, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java index d6c938f36..efb92235f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java @@ -1,16 +1,16 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.utils.*; - -import java.util.Collections; -import java.util.Collection; -import java.util.Arrays; - -import net.sf.samtools.SAMSequenceRecord; -import net.sf.samtools.SAMRecord; -import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.picard.reference.ReferenceSequence; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMSequenceRecord; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; /** * User: hanna * Date: May 22, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java index feed2ab85..39c632539 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java index a0ea32f9b..803bd885b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java @@ -1,15 +1,14 @@ package org.broadinstitute.sting.gatk.datasources.providers; +import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; -import java.util.List; import java.util.Collection; - -import net.sf.picard.reference.IndexedFastaSequenceFile; +import java.util.List; /** * User: hanna * Date: May 8, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java index a9e04e357..de938e845 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java @@ -24,9 +24,6 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; -import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.utils.exceptions.StingException; import java.io.File; @@ -35,9 +32,7 @@ import java.io.IOException; import java.nio.ByteBuffer; import java.nio.ByteOrder; import java.nio.channels.FileChannel; -import java.util.ArrayList; import java.util.Iterator; -import java.util.List; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java index 34693d501..521bcd5a3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java @@ -39,12 +39,7 @@ import java.io.RandomAccessFile; import java.nio.ByteBuffer; import java.nio.ByteOrder; import java.nio.channels.FileChannel; -import java.util.ArrayList; -import java.util.BitSet; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; +import java.util.*; /** * Writes schedules for a single BAM file to a target output file. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java index 266232c0f..467aebac5 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java @@ -26,20 +26,10 @@ package org.broadinstitute.sting.gatk.datasources.reads; import net.sf.picard.util.PeekableIterator; import net.sf.samtools.GATKBAMFileSpan; -import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import java.io.File; -import java.util.ArrayList; -import java.util.Collections; -import java.util.Comparator; -import java.util.HashMap; -import java.util.Iterator; -import java.util.LinkedList; -import java.util.List; -import java.util.Map; -import java.util.NoSuchElementException; +import java.util.*; /** * Assign intervals to the most appropriate blocks, keeping as little as possible in memory at once. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java index c014c1995..e4141f61c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java @@ -29,19 +29,11 @@ import net.sf.samtools.GATKBAMFileSpan; import net.sf.samtools.SAMFileSpan; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; -import java.util.SortedMap; -import java.util.TreeMap; +import java.util.*; /** * Represents a small section of a BAM file, and every associated interval. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java index 8ebb8b1a8..5d0c38b78 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java @@ -23,24 +23,18 @@ */ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.Bin; - -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKBin; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.LinearIndex; -import net.sf.samtools.SAMException; -import net.sf.samtools.util.RuntimeIOException; +import net.sf.samtools.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; import java.io.FileInputStream; import java.io.IOException; -import java.lang.ref.SoftReference; import java.nio.ByteBuffer; import java.nio.ByteOrder; import java.nio.channels.FileChannel; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; /** * A basic interface for querying BAM indices. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java index f9b998a60..daf1b77e3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java @@ -24,11 +24,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.Bin; -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKBin; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.LinearIndex; +import net.sf.samtools.*; import java.util.ArrayList; import java.util.Collections; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java index fc3f76ab7..4ddf28dce 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java @@ -35,16 +35,7 @@ import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.Iterator; -import java.util.LinkedList; -import java.util.List; -import java.util.Map; -import java.util.NoSuchElementException; -import java.util.PriorityQueue; -import java.util.Queue; +import java.util.*; /** * Shard intervals based on position within the BAM file. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java index 26af890b4..19d33aa6b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.reads; +import net.sf.samtools.SAMFileSpan; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; @@ -7,8 +8,6 @@ import org.broadinstitute.sting.utils.Utils; import java.util.List; import java.util.Map; -import net.sf.samtools.SAMFileSpan; - /** * Handles locus shards of BAM information. * @author aaron diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java index 950d67428..a5ca07853 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java @@ -24,17 +24,18 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.GATKBAMFileSpan; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMFileSpan; +import net.sf.samtools.SAMSequenceRecord; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import java.util.*; - -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMSequenceRecord; -import net.sf.samtools.SAMFileSpan; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; /** * A sharding strategy for loci based on reading of the index. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java index 7579c22f6..278eeb898 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.datasources.reads; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.GenomeLoc; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java index 10228ecd7..28b737f28 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java @@ -4,8 +4,8 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import java.util.Iterator; -import java.util.NoSuchElementException; import java.util.List; +import java.util.NoSuchElementException; /** * Create a giant shard representing all the data in the input BAM(s). diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java index 9aecd7779..4d9c9092d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java @@ -1,15 +1,17 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter; - -import java.util.*; - import net.sf.samtools.SAMFileSpan; import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import java.util.ArrayList; +import java.util.Collection; +import java.util.List; +import java.util.Map; + /** * * User: aaron diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java index da70a615b..c2235ec73 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java @@ -25,12 +25,11 @@ package org.broadinstitute.sting.gatk.datasources.reads; import net.sf.samtools.SAMFileSpan; - -import java.util.*; - import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import java.util.*; + /** * The sharding strategy for reads using a simple counting mechanism. Each read shard * has a specific number of reads (default to 10K) which is configured in the constructor. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index c2aa5f18e..6064806f3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -24,21 +24,19 @@ package org.broadinstitute.sting.gatk.datasources.reads; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.picard.sam.MergingSamRecordIterator; +import net.sf.picard.sam.SamFileHeaderMerger; import net.sf.samtools.*; import net.sf.samtools.util.CloseableIterator; -import net.sf.picard.filter.SamRecordFilter; -import net.sf.picard.sam.SamFileHeaderMerger; -import net.sf.picard.sam.MergingSamRecordIterator; -import net.sf.picard.reference.IndexedFastaSequenceFile; - import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.DownsamplingMethod; -import org.broadinstitute.sting.gatk.filters.ReadFilter; -import org.broadinstitute.sting.gatk.iterators.*; -import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.ReadMetrics; +import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; +import org.broadinstitute.sting.gatk.filters.ReadFilter; +import org.broadinstitute.sting.gatk.iterators.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.baq.BAQ; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java index 418f5d3ee..f8d941784 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java @@ -2,17 +2,13 @@ package org.broadinstitute.sting.gatk.datasources.reads; import net.sf.samtools.SAMFileSpan; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadProperties; +import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.HasGenomeLocation; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.io.Serializable; import java.util.Collections; import java.util.List; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java index fa733ce12..780b41ef7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java @@ -1,10 +1,10 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.SAMSequenceDictionary; import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java index ae0f1cf43..07c13a76e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java @@ -25,17 +25,17 @@ package org.broadinstitute.sting.gatk.datasources.reads.utilities; -import org.broadinstitute.sting.commandline.CommandLineProgram; +import net.sf.samtools.BAMIndex; +import net.sf.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.instrumentation.Sizeof; import java.io.File; import java.lang.reflect.Field; -import java.util.Map; import java.util.List; - -import net.sf.samtools.*; +import java.util.Map; /** * diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java index f03e2a44f..54de04379 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java @@ -24,12 +24,12 @@ package org.broadinstitute.sting.gatk.datasources.reads.utilities; -import org.broadinstitute.sting.commandline.CommandLineProgram; -import org.broadinstitute.sting.commandline.Argument; -import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileWriterFactory; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.CommandLineProgram; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java index df7dccaa9..773541d11 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java @@ -24,7 +24,6 @@ package org.broadinstitute.sting.gatk.datasources.reads.utilities; -import net.sf.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.CommandLineProgram; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java index c2d64ddd8..ef69a8e5f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java @@ -25,16 +25,15 @@ package org.broadinstitute.sting.gatk.datasources.reference; -import net.sf.picard.reference.ReferenceSequenceFileFactory; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import net.sf.picard.reference.FastaSequenceIndexBuilder; -import net.sf.picard.sam.CreateSequenceDictionary; -import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.FastaSequenceIndex; +import net.sf.picard.reference.FastaSequenceIndexBuilder; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.picard.sam.CreateSequenceDictionary; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.file.FSLockWithShared; import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java index 934f4f997..21f58d480 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java @@ -28,11 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; +import java.util.*; /** * A pool of open resources, all of which can create a closeable iterator. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java index 0a5981a1b..067bf3f72 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java @@ -3,11 +3,10 @@ package org.broadinstitute.sting.gatk.datasources.sample; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.yaml.snakeyaml.TypeDescription; import org.yaml.snakeyaml.Yaml; import org.yaml.snakeyaml.constructor.Constructor; diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java index a1419ba70..5dbd90405 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java @@ -1,15 +1,20 @@ package org.broadinstitute.sting.gatk.examples; -import net.sf.samtools.*; -import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.gatk.contexts.*; -import org.broadinstitute.sting.utils.pileup.*; +import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import java.util.*; import java.io.PrintStream; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; /** * Computes the coverage per sample. diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java index b96d0ffbf..26205a203 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java @@ -25,6 +25,8 @@ package org.broadinstitute.sting.gatk.examples; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -32,8 +34,6 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypePriors; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java index 3e335733d..b23782563 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java @@ -25,18 +25,18 @@ package org.broadinstitute.sting.gatk.executive; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; -import java.util.List; import java.util.Iterator; +import java.util.List; /** * Manages the */ diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index 8a27e008c..59fb4aa9e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -1,27 +1,27 @@ package org.broadinstitute.sting.gatk.executive; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.io.*; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.gatk.io.OutputTracker; +import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; +import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor; -import java.util.Queue; -import java.util.LinkedList; import java.util.Collection; -import java.util.concurrent.Executors; +import java.util.LinkedList; +import java.util.Queue; import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; import java.util.concurrent.Future; import java.util.concurrent.FutureTask; -import net.sf.picard.reference.IndexedFastaSequenceFile; - /** * A microscheduler that schedules shards according to a tree-like structure. * Requires a special walker tagged with a 'TreeReducible' interface. diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java index 4cb571c45..9466fdf75 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java @@ -1,22 +1,21 @@ package org.broadinstitute.sting.gatk.executive; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.io.DirectOutputTracker; import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.gatk.walkers.Walker; import java.util.Collection; -import net.sf.picard.reference.IndexedFastaSequenceFile; - /** A micro-scheduling manager for single-threaded execution of a traversal. */ public class LinearMicroScheduler extends MicroScheduler { diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index cfe0f8187..23e5769f1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -25,26 +25,18 @@ package org.broadinstitute.sting.gatk.executive; +import net.sf.picard.reference.IndexedFastaSequenceFile; import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy; +import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.io.OutputTracker; +import org.broadinstitute.sting.gatk.iterators.NullSAMIterator; +import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.traversals.*; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.gatk.iterators.NullSAMIterator; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.ReadMetrics; - -import java.io.FileNotFoundException; -import java.io.FileOutputStream; -import java.io.PrintStream; -import java.lang.management.ManagementFactory; -import java.util.*; - -import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.threading.*; @@ -52,6 +44,11 @@ import org.broadinstitute.sting.utils.threading.*; import javax.management.JMException; import javax.management.MBeanServer; import javax.management.ObjectName; +import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.PrintStream; +import java.lang.management.ManagementFactory; +import java.util.Collection; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java b/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java index 76e0c1c8a..7be37a616 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java @@ -1,10 +1,9 @@ package org.broadinstitute.sting.gatk.executive; import org.broadinstitute.sting.gatk.io.storage.Storage; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import java.util.Collection; import java.util.ArrayList; +import java.util.Collection; /** * User: hanna diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java index 151a1ba26..7aac70b47 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.executive; -import java.util.Queue; -import java.util.List; import java.util.ArrayList; import java.util.LinkedList; +import java.util.List; +import java.util.Queue; import java.util.concurrent.Future; /** * User: hanna diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index b78a4edc9..6136bd68d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.executive; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.traversals.TraversalEngine; import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker; -import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.sting.gatk.traversals.TraversalEngine; import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.concurrent.Callable; diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java index 8fb4adb5d..d36a3b576 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java @@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.concurrent.Callable; -import java.util.concurrent.Future; import java.util.concurrent.ExecutionException; +import java.util.concurrent.Future; /** * User: hanna * Date: Apr 29, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java index 5c341bb02..cfbce58ee 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java @@ -1,17 +1,20 @@ package org.broadinstitute.sting.gatk.executive; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.gatk.iterators.*; +import net.sf.picard.util.PeekableIterator; import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; - -import java.util.*; - -import net.sf.picard.util.PeekableIterator; +import org.broadinstitute.sting.gatk.datasources.reads.Shard; +import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource; +import org.broadinstitute.sting.gatk.iterators.LocusIterator; +import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState; +import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import java.util.Iterator; +import java.util.List; +import java.util.NoSuchElementException; + /** * Buffer shards of data which may or may not contain multiple loci into * iterators of all data which cover an interval. Its existence is an homage diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java index b8a3ee977..0987c5d74 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java @@ -24,8 +24,10 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; -import net.sf.samtools.*; +import net.sf.samtools.Cigar; +import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; +import net.sf.samtools.SAMRecord; /** * Filter out reads with wonky cigar strings. diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java index 3b988c8fb..8596e18eb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java @@ -24,7 +24,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java b/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java index 84390c173..03fc2063b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java @@ -23,17 +23,16 @@ */ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.util.CloserUtil; - -import java.util.Iterator; -import java.util.NoSuchElementException; -import java.util.Collection; - +import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; import net.sf.samtools.util.CloseableIterator; -import net.sf.picard.filter.SamRecordFilter; +import net.sf.samtools.util.CloserUtil; import org.broadinstitute.sting.gatk.ReadMetrics; +import java.util.Collection; +import java.util.Iterator; +import java.util.NoSuchElementException; + /** * Filtering Iterator which takes a filter and an iterator and iterates * through only those records which are not rejected by the filter. diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java index fb3c38582..589910fc7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; /* diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java index b7806524a..cd77a9e7e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java @@ -24,7 +24,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java b/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java index cda08fb66..67f82235d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java @@ -25,11 +25,8 @@ package org.broadinstitute.sting.gatk.filters; -import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.classloader.PluginManager; -import net.sf.picard.filter.SamRecordFilter; - import java.util.Collection; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java index 4deeb09ee..74deace9a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java @@ -24,8 +24,8 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java index bcd473b15..75369b306 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java @@ -25,7 +25,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java index cecbedda8..1afec36d1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java @@ -24,7 +24,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.util.QualityUtil; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java index 584783d34..7bcee033f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java index 8a2fd5af3..cd31da61a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java @@ -25,7 +25,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java index d5d40ec38..490a55040 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java @@ -24,7 +24,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java index fc21538e8..29738e499 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; /* diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java index cfbba0383..31c2144ce 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java @@ -24,7 +24,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java index dcddebd55..8ad91ac1c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java @@ -25,9 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; - import org.broadinstitute.sting.utils.sam.ReadUtils; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java index 691fd95f0..30b2f828d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java @@ -25,11 +25,9 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; - -import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.utils.sam.ReadUtils; /** * Filter out PL matching reads. diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java index 4ef88402d..81044b888 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java @@ -1,14 +1,12 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; -import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMReadGroupRecord; - -import java.util.Set; -import java.util.HashSet; - +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.UserException; +import java.util.HashSet; +import java.util.Set; + /** * Created by IntelliJ IDEA. * User: asivache diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java index 1d74ee20e..227637761 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java @@ -1,7 +1,6 @@ package org.broadinstitute.sting.gatk.filters; import net.sf.picard.filter.SamRecordFilter; -import net.sf.samtools.SAMFileHeader; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java index 69ebc8b04..0e5e8800c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java @@ -25,17 +25,16 @@ package org.broadinstitute.sting.gatk.filters; -import java.util.*; -import java.util.Map.Entry; -import java.io.File; -import java.io.FileNotFoundException; - -import net.sf.picard.filter.SamRecordFilter; -import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMReadGroupRecord; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; +import java.io.File; +import java.io.FileNotFoundException; +import java.util.*; +import java.util.Map.Entry; + /** * Removes records matching the read group tag and exact match string. * For example, this filter value: diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java index 1b2a77f45..16eeed3cc 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java @@ -25,7 +25,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java index 682b22b1f..99d6bc154 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java @@ -25,9 +25,8 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; -import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMReadGroupRecord; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java index 05b472036..2f93cbcae 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java @@ -25,9 +25,8 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMReadGroupRecord; -import net.sf.picard.filter.SamRecordFilter; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java index ac4f4853a..e7ee345d2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java @@ -24,7 +24,6 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; import net.sf.samtools.SAMRecord; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java index 865528688..658a28fbd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.io; -import org.broadinstitute.sting.gatk.io.stubs.Stub; -import org.broadinstitute.sting.gatk.io.storage.StorageFactory; import org.broadinstitute.sting.gatk.io.storage.Storage; +import org.broadinstitute.sting.gatk.io.storage.StorageFactory; +import org.broadinstitute.sting.gatk.io.stubs.Stub; /** * Maps creation of storage directly to output streams in parent. diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java index b68013aa4..f39ba2d8d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java @@ -26,20 +26,20 @@ package org.broadinstitute.sting.gatk.io; import net.sf.samtools.SAMFileReader; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.commandline.ArgumentSource; -import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder; -import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.sting.gatk.io.storage.Storage; +import org.broadinstitute.sting.gatk.io.storage.StorageFactory; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.gatk.io.stubs.Stub; -import org.broadinstitute.sting.gatk.io.storage.StorageFactory; -import org.broadinstitute.sting.gatk.io.storage.Storage; +import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.sting.utils.classloader.JVMUtils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder; -import java.io.*; +import java.io.OutputStream; import java.lang.reflect.Field; -import java.util.Map; import java.util.HashMap; +import java.util.Map; /** * Manages the output and err streams that are created specifically for walker diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java b/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java index 8701ecf3c..a9a74925d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.io; -import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMFileWriter; /** * A writer that will allow unsorted BAM files to be written diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java index 36960246a..999deddd1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java @@ -25,15 +25,16 @@ package org.broadinstitute.sting.gatk.io; -import org.broadinstitute.sting.gatk.io.stubs.Stub; -import org.broadinstitute.sting.gatk.io.storage.StorageFactory; -import org.broadinstitute.sting.gatk.io.storage.Storage; import org.broadinstitute.sting.gatk.executive.OutputMergeTask; +import org.broadinstitute.sting.gatk.io.storage.Storage; +import org.broadinstitute.sting.gatk.io.storage.StorageFactory; +import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.utils.exceptions.UserException; -import java.util.*; import java.io.File; import java.io.IOException; +import java.util.HashMap; +import java.util.Map; /** * An output tracker that can either track its output per-thread or directly, diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java index 4dc976289..56c9c0465 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java @@ -25,14 +25,14 @@ package org.broadinstitute.sting.gatk.io.storage; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.*; +import java.nio.channels.Channels; import java.nio.channels.FileChannel; import java.nio.channels.WritableByteChannel; -import java.nio.channels.Channels; public class OutputStreamStorage extends OutputStream implements Storage { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java index 610db1d76..cb8786be1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java @@ -27,17 +27,16 @@ package org.broadinstitute.sting.gatk.io.storage; import net.sf.samtools.*; import net.sf.samtools.util.CloseableIterator; - -import java.io.*; -import java.lang.reflect.InvocationTargetException; -import java.lang.reflect.Method; - import net.sf.samtools.util.RuntimeIOException; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.SimplifyingSAMFileWriter; +import java.io.File; +import java.lang.reflect.InvocationTargetException; +import java.lang.reflect.Method; + /** * Provides temporary storage for SAMFileWriters. * diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java index ee5c56524..66907dd6b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.io.storage; -import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; +import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java index 74176ec35..1da03e9c2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java @@ -1,16 +1,21 @@ package org.broadinstitute.sting.gatk.io.storage; +import net.sf.samtools.util.BlockCompressedOutputStream; import org.apache.log4j.Logger; import org.broad.tribble.source.BasicFeatureSource; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; - -import java.io.*; - -import net.sf.samtools.util.BlockCompressedOutputStream; +import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.io.File; +import java.io.IOException; +import java.io.OutputStream; +import java.io.PrintStream; /** * Provides temporary and permanent storage for genotypes in VCF format. diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java index 00e78f391..8bc97c886 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java @@ -30,8 +30,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.io.OutputStream; import java.io.File; +import java.io.OutputStream; import java.lang.reflect.Constructor; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java index 5cf84c5a2..27bcb8a1c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java @@ -27,9 +27,9 @@ package org.broadinstitute.sting.gatk.io.stubs; import org.broadinstitute.sting.gatk.io.OutputTracker; -import java.io.OutputStream; -import java.io.IOException; import java.io.File; +import java.io.IOException; +import java.io.OutputStream; /** * A stub for routing and management of anything backed by an OutputStream. diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java index d847015ed..f124c2302 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java @@ -24,14 +24,14 @@ package org.broadinstitute.sting.gatk.io.stubs; -import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor; -import org.broadinstitute.sting.commandline.ArgumentSource; +import net.sf.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.ArgumentMatches; +import org.broadinstitute.sting.commandline.ArgumentSource; +import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor; import org.broadinstitute.sting.commandline.ParsingEngine; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import net.sf.samtools.SAMFileReader; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java index a9a272220..38640eda0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java @@ -25,18 +25,17 @@ package org.broadinstitute.sting.gatk.io.stubs; +import net.sf.samtools.SAMFileWriter; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import net.sf.samtools.SAMFileWriter; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import java.lang.annotation.Annotation; -import java.util.List; -import java.util.Arrays; import java.io.File; import java.io.OutputStream; +import java.lang.annotation.Annotation; +import java.util.Arrays; +import java.util.List; /** * Insert a SAMFileWriterStub instead of a full-fledged concrete OutputStream implementations. diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java index f5c1e0efc..d8e59a3dd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java @@ -25,20 +25,19 @@ package org.broadinstitute.sting.gatk.io.stubs; +import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMFileHeader; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.gatk.io.OutputTracker; +import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; +import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; import java.io.OutputStream; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.baq.BAQ; - /** * A stub for routing and management of SAM file reading and writing. * diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java index 7521e754d..615841f02 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -25,14 +25,17 @@ package org.broadinstitute.sting.gatk.io.stubs; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; import java.io.OutputStream; -import java.util.*; +import java.util.Arrays; +import java.util.Collection; +import java.util.HashSet; +import java.util.List; /** * Injects new command-line arguments into the system providing support for the genotype writer. diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java index 1a79d2785..bb84f9457 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java @@ -25,19 +25,19 @@ package org.broadinstitute.sting.gatk.io.stubs; -import java.io.File; -import java.io.PrintStream; -import java.io.OutputStream; -import java.util.Collection; - -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.gatk.CommandLineExecutable; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.utils.classloader.JVMUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.io.File; +import java.io.OutputStream; +import java.io.PrintStream; +import java.util.Collection; /** * A stub for routing and management of genotype reading and writing. diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java index b5643f834..478675f9d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java @@ -1,13 +1,11 @@ package org.broadinstitute.sting.gatk.iterators; +import net.sf.picard.sam.MergingSamRecordIterator; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMRecord; -import net.sf.picard.sam.MergingSamRecordIterator; import java.util.Iterator; -import org.broadinstitute.sting.gatk.ReadProperties; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java index f3a060be1..7eaf4be41 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java @@ -26,12 +26,11 @@ package org.broadinstitute.sting.gatk.iterators; import net.sf.samtools.SAMRecord; import net.sf.samtools.util.CloseableIterator; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.Queue; import java.util.LinkedList; import java.util.NoSuchElementException; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import java.util.Queue; /** * Buffers access to a large stream of reads, replenishing the buffer only when the reads diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java index 1342f11fd..835748ff0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java @@ -1,11 +1,10 @@ package org.broadinstitute.sting.gatk.iterators; import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import java.util.Iterator; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; - public class DownsampleIterator implements StingSAMIterator { diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java index aa376a12a..240564d34 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java @@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.iterators; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import java.util.NoSuchElementException; import java.util.Iterator; +import java.util.NoSuchElementException; /** * User: hanna * Date: May 12, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java index 30c1cf512..e177984ca 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java @@ -1,11 +1,10 @@ package org.broadinstitute.sting.gatk.iterators; import net.sf.samtools.util.CloseableIterator; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import java.util.Iterator; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; - /** * Iterator that traverses a SAM File, accumulating information on a per-locus basis */ diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java index 4e58813f5..e13c5a764 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java @@ -25,19 +25,27 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.*; import net.sf.picard.util.PeekableIterator; +import net.sf.samtools.Cigar; +import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; +import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.ReadProperties; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.DownsamplingMethod; import org.broadinstitute.sting.gatk.DownsampleType; +import org.broadinstitute.sting.gatk.DownsamplingMethod; +import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.ReservoirDownsampler; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.pileup.*; +import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileupImpl; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.sam.ReadUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java index ff458467f..21b71c9e6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.iterators; -import org.broadinstitute.sting.gatk.ReadProperties; import net.sf.samtools.SAMRecord; import java.util.Iterator; diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java index c2d3976ea..cc499b247 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java @@ -25,7 +25,6 @@ package org.broadinstitute.sting.gatk.iterators; -import org.broadinstitute.sting.gatk.ReadProperties; import net.sf.samtools.SAMRecord; import net.sf.samtools.util.CloseableIterator; diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java index 239392eec..2f30d12a8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java @@ -1,13 +1,8 @@ package org.broadinstitute.sting.gatk.iterators; import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMTag; -import net.sf.samtools.SAMReadGroupRecord; -import org.broadinstitute.sting.gatk.ReadProperties; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.apache.log4j.Logger; - -import java.util.List; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; /** * An iterator which does post-processing of a read, including potentially wrapping diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java index d294993d4..1b248d097 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java @@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.iterators; import net.sf.samtools.SAMRecord; import net.sf.samtools.util.CloseableIterator; -import org.broadinstitute.sting.gatk.ReadProperties; /** * * User: aaron diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java index a51ca9292..69c0b3e0a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java @@ -26,19 +26,16 @@ package org.broadinstitute.sting.gatk.phonehome; import org.apache.log4j.Level; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.CommandLineUtils; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.jets3t.service.S3Service; import org.jets3t.service.S3ServiceException; import org.jets3t.service.impl.rest.httpclient.RestS3Service; -import org.jets3t.service.model.S3Bucket; import org.jets3t.service.model.S3Object; import org.jets3t.service.security.AWSCredentials; import org.simpleframework.xml.Element; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java index fa0c323b5..ce924fd87 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java @@ -25,17 +25,17 @@ package org.broadinstitute.sting.gatk.refdata; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.gatk.iterators.PushbackIterator; +import java.io.File; +import java.io.FileNotFoundException; +import java.lang.reflect.Constructor; import java.util.Iterator; import java.util.regex.Pattern; -import java.io.FileNotFoundException; -import java.io.File; -import java.lang.reflect.Constructor; /** * This is a low-level iterator designed to provide system-wide generic support for reading record-oriented data diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java index cff97e4ee..59b273d38 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java @@ -2,9 +2,9 @@ package org.broadinstitute.sting.gatk.refdata; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.GenomeLoc; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index 43bf6f8e0..d03b122e2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.refdata; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java index b3cb22a03..b7437e6e8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java @@ -6,9 +6,9 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.Iterator; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index c7c0468e7..1d622e2c7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -3,17 +3,13 @@ package org.broadinstitute.sting.gatk.refdata; import org.broad.tribble.Feature; import org.broad.tribble.dbsnp.DbSNPFeature; import org.broad.tribble.gelitext.GeliTextFeature; -import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.MutableGenotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java index 59cd14a22..6bba754be 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java @@ -25,12 +25,6 @@ package org.broadinstitute.sting.gatk.refdata.features.annotator; -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.util.ArrayList; -import java.util.StringTokenizer; - import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broad.tribble.exception.CodecLineParsingException; @@ -41,6 +35,12 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.util.ArrayList; +import java.util.StringTokenizer; + public class AnnotatorInputTableCodec implements ReferenceDependentFeatureCodec { private static Logger logger = Logger.getLogger(AnnotatorInputTableCodec.class); diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java index d97e378fb..d12badd28 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.gatk.refdata.features.annotator; +import org.broad.tribble.Feature; + import java.util.ArrayList; import java.util.Collections; import java.util.HashMap; import java.util.Map; -import org.broad.tribble.Feature; - /** * This class represents a single record in an AnnotatorInputTable. */ diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java index 7f97451cf..5e536d4c1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java @@ -26,19 +26,19 @@ package org.broadinstitute.sting.gatk.refdata.features.beagle; import org.broad.tribble.Feature; +import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.LineReader; +import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; + import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; -import java.util.regex.Matcher; import java.util.regex.Pattern; -import org.broad.tribble.exception.CodecLineParsingException; -import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; public class BeagleCodec implements ReferenceDependentFeatureCodec { private String[] header; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java index c7bf86569..e6832754d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java @@ -25,14 +25,11 @@ package org.broadinstitute.sting.gatk.refdata.features.beagle; import org.broad.tribble.Feature; - +import org.broadinstitute.sting.utils.variantcontext.Allele; import java.util.ArrayList; import java.util.Map; -import net.sf.samtools.util.StringUtil; -import org.broadinstitute.sting.utils.variantcontext.Allele; - public class BeagleFeature implements Feature { private String chr; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java index 4648efd1e..d12114f9a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java @@ -4,9 +4,8 @@ import org.broad.tribble.Feature; import org.broadinstitute.sting.gatk.refdata.Transcript; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java index 00b7c45d9..43e2c3ff5 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java @@ -25,15 +25,15 @@ package org.broadinstitute.sting.gatk.refdata.features.sampileup; -import org.broad.tribble.FeatureCodec; import org.broad.tribble.Feature; +import org.broad.tribble.FeatureCodec; import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.readers.LineReader; import org.broad.tribble.util.ParsingUtils; import java.util.ArrayList; -import java.util.regex.Pattern; import java.util.regex.Matcher; +import java.util.regex.Pattern; import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java index a794c2704..378f26934 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java @@ -25,12 +25,11 @@ package org.broadinstitute.sting.gatk.refdata.features.sampileup; +import net.sf.samtools.util.StringUtil; import org.broad.tribble.Feature; import java.util.List; -import net.sf.samtools.util.StringUtil; - /** * A tribble feature representing a SAM pileup. * diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java index 15f559d46..039b8adde 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java @@ -24,14 +24,14 @@ package org.broadinstitute.sting.gatk.refdata.features.samread; +import net.sf.samtools.Cigar; +import net.sf.samtools.TextCigarCodec; +import net.sf.samtools.util.StringUtil; import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.readers.LineReader; import org.broad.tribble.util.ParsingUtils; -import net.sf.samtools.util.StringUtil; -import net.sf.samtools.TextCigarCodec; -import net.sf.samtools.Cigar; /** * Decodes a simple SAM text string. diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java index b831606a3..745ccdd9f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java @@ -1,13 +1,8 @@ package org.broadinstitute.sting.gatk.refdata.features.table; import org.broad.tribble.Feature; -import org.broad.tribble.readers.LineReader; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.UserException; -import java.io.IOException; -import java.util.ArrayList; import java.util.Arrays; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java index 6f0a712bf..ab1ac59d8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java @@ -1,16 +1,14 @@ package org.broadinstitute.sting.gatk.refdata.features.table; import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; import org.broad.tribble.readers.LineReader; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.interval.IntervalUtils; import java.io.IOException; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; /** * implementation of a simple table (tab or comma delimited format) input files diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java index 4b4ebe450..ca73ee960 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata.features.table; import org.broad.tribble.Feature; import org.broadinstitute.sting.utils.GenomeLoc; -import java.util.*; +import java.util.List; /** * A feature representing a single row out of a text table diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java index 5bb65f9a2..085d6b5b3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java @@ -10,7 +10,6 @@ import org.broad.tribble.util.LittleEndianOutputStream; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java index 19050ae11..731df997d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java @@ -28,7 +28,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.utils.GenomeLoc; import java.io.IOException; -import java.util.Iterator; /** * @author aaron diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java index 3b9f8243f..ba1ca674e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java @@ -35,8 +35,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; import java.io.IOException; -import java.lang.reflect.Type; -import java.util.Iterator; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java index c2057ad5e..19c91be1b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java @@ -42,15 +42,17 @@ import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.SequenceDictionaryUtils; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.file.FSLockWithShared; import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException; import org.broadinstitute.sting.utils.instrumentation.Sizeof; -import java.io.*; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java index 462bf98df..104ba87b5 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java @@ -28,8 +28,6 @@ import org.broad.tribble.Feature; import org.broad.tribble.iterators.CloseableTribbleIterator; import org.broadinstitute.sting.utils.GenomeLocParser; -import java.util.Iterator; - /** * diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java index 1553402a5..59e8471a3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java @@ -28,8 +28,6 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.HasGenomeLocation; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java index 83aa5f056..96086598a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java @@ -2,12 +2,8 @@ package org.broadinstitute.sting.gatk.refdata.utils; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.util.CloseableIterator; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.utils.GenomeLoc; -import java.util.Iterator; -import java.util.List; - /** * @author aaron *

diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java index 101784d97..fc7f7c58f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.refdata.utils; +import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.bed.BedParser; -import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import java.util.Iterator; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java index 75e7c1a32..3201769e0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java @@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.refdata.utils.helpers; import net.sf.samtools.util.SequenceUtil; import org.broad.tribble.annotation.Strand; import org.broad.tribble.dbsnp.DbSNPFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index e1085c6b2..89a179d0e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.gatk.traversals; import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.ReadMetrics; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -38,7 +38,10 @@ import java.io.File; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.PrintStream; -import java.util.*; +import java.util.Arrays; +import java.util.LinkedList; +import java.util.List; +import java.util.Map; public abstract class TraversalEngine,ProviderType extends ShardDataProvider> { // Time in milliseconds since we initialized this engine diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java index 89ff688a7..1ba48ca5f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java @@ -28,12 +28,11 @@ package org.broadinstitute.sting.gatk.traversals; import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.datasources.providers.ReadView; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ReadView; import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.gatk.walkers.DuplicateWalker; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java index 240176f2f..232989fb0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java @@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java index f15a20cd3..196d54036 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java @@ -1,16 +1,18 @@ package org.broadinstitute.sting.gatk.traversals; -import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.ReadPairWalker; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMRecordCoordinateComparator; +import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ReadView; import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.apache.log4j.Logger; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMRecordCoordinateComparator; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.ReadPairWalker; +import org.broadinstitute.sting.gatk.walkers.Requires; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; /** * Traverse over a collection of read pairs, assuming that a given shard will contain all pairs. diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index 670676b48..06e4539c4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -2,14 +2,16 @@ package org.broadinstitute.sting.gatk.traversals; import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.WalkerManager; import org.broadinstitute.sting.gatk.ReadMetrics; +import org.broadinstitute.sting.gatk.WalkerManager; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.providers.*; +import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrderedView; +import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView; +import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ReadView; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLoc; /* diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java index a29e51189..2541921e9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java @@ -1,11 +1,6 @@ package org.broadinstitute.sting.gatk.walkers; -import java.lang.annotation.Documented; -import java.lang.annotation.Inherited; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; -import java.lang.annotation.ElementType; +import java.lang.annotation.*; /** * User: hanna * Date: May 19, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java index 99dd46cbe..03097887d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java @@ -1,11 +1,6 @@ package org.broadinstitute.sting.gatk.walkers; -import java.lang.annotation.Documented; -import java.lang.annotation.Inherited; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; -import java.lang.annotation.ElementType; +import java.lang.annotation.*; /** * User: hanna diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java index 25455b587..8fa6a4c1b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java @@ -1,11 +1,6 @@ package org.broadinstitute.sting.gatk.walkers; -import java.lang.annotation.Documented; -import java.lang.annotation.Inherited; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; -import java.lang.annotation.ElementType; +import java.lang.annotation.*; /** * User: hanna * Date: May 14, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java index 1a3f87a7a..ca4e3f5e3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java @@ -25,29 +25,29 @@ package org.broadinstitute.sting.gatk.walkers; -import net.sf.samtools.*; -import net.sf.picard.reference.ReferenceSequenceFileFactory; -import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.picard.reference.ReferenceSequence; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import net.sf.picard.reference.ReferenceSequenceFile; +import net.sf.picard.reference.ReferenceSequenceFileFactory; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.util.StringUtil; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.clipreads.ClippingOp; import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation; import org.broadinstitute.sting.utils.clipreads.ReadClipper; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.utils.sam.ReadUtils; -import java.util.*; -import java.util.regex.Pattern; -import java.util.regex.Matcher; import java.io.File; import java.io.PrintStream; - -import net.sf.samtools.util.StringUtil; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; /** * This ReadWalker provides simple, yet powerful read clipping capabilities. It allows the user to clip bases in reads diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java index 1fc606f07..4bfedb672 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java @@ -1,16 +1,13 @@ package org.broadinstitute.sting.gatk.walkers; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter; import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter; +import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter; import org.broadinstitute.sting.utils.GenomeLoc; import java.util.List; import java.util.Set; -import java.util.Arrays; - -import net.sf.samtools.SAMRecord; -import net.sf.picard.filter.SamRecordFilter; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java index a272150c7..56287df31 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java @@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.walkers; import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java index 13a55eaac..fcfcb81b5 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import java.io.PrintStream; import java.text.DecimalFormat; import java.text.NumberFormat; -import java.io.PrintStream; /* diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java index c0f469973..68bea4dba 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java @@ -28,13 +28,12 @@ import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; import java.io.PrintStream; -import java.util.*; +import java.util.List; /** * Walks along reference and calculates the GC content for each interval. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java index fc4b403c5..b0b2687f4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java @@ -1,9 +1,12 @@ package org.broadinstitute.sting.gatk.walkers; -import org.broadinstitute.sting.gatk.filters.*; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter; +import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckReadFilter; +import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter; +import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index 84d868c1a..508d1f6ee 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -26,22 +26,22 @@ package org.broadinstitute.sting.gatk.walkers; import org.broad.tribble.dbsnp.DbSNPFeature; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import java.io.PrintStream; import java.util.ArrayList; import java.util.List; -import java.io.PrintStream; /** * Prints the alignment in the pileup format. In the pileup format, each line represents a genomic position, diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java index 9ac3fc0e6..158992a22 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java @@ -25,15 +25,15 @@ package org.broadinstitute.sting.gatk.walkers; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.commandline.Output; -import java.util.Iterator; import java.io.PrintStream; +import java.util.Iterator; /** * Prints out all of the RODs in the input data set. Data is rendered using the toString() method diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java index 07938d322..a189c00b5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java @@ -28,14 +28,12 @@ package org.broadinstitute.sting.gatk.walkers; import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.utils.baq.BAQ; -import java.io.PrintStream; - /** * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear * in the input file. It can dynamically merge the contents of multiple input BAM files, resulting diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java index a5486fd9a..db2038aa3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java index 6c1e64c4e..e9a381a85 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java @@ -1,11 +1,6 @@ package org.broadinstitute.sting.gatk.walkers; -import java.lang.annotation.Documented; -import java.lang.annotation.Inherited; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; -import java.lang.annotation.ElementType; +import java.lang.annotation.*; /** * User: hanna * Date: May 19, 2009 diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java index 014acff9c..486d233b7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java @@ -25,14 +25,20 @@ package org.broadinstitute.sting.gatk.walkers; -import net.sf.samtools.*; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMFileWriter; +import net.sf.samtools.SAMReadGroupRecord; +import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.utils.sam.ReadUtils; -import java.util.*; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * Divides the input data set into separate BAM files, one for each sample in the input data set. The split diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java index f0ba8bb46..384742302 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java @@ -25,14 +25,14 @@ package org.broadinstitute.sting.gatk.walkers; -import java.util.List; - +import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.filters.MalformedReadFilter; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.collections.Pair; -import org.apache.log4j.Logger; + +import java.util.List; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java index 0e4d40675..4d46607e5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java @@ -1,10 +1,6 @@ package org.broadinstitute.sting.gatk.walkers; -import java.lang.annotation.Documented; -import java.lang.annotation.ElementType; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; +import java.lang.annotation.*; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java index 0b718071d..9827fdf09 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java @@ -25,7 +25,10 @@ package org.broadinstitute.sting.gatk.walkers; -import java.lang.annotation.*; +import java.lang.annotation.Documented; +import java.lang.annotation.Inherited; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; /** * Describes the size of the window into the genome. Has differing semantics based on diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index b02dcd8e2..3144098a8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -25,21 +25,21 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; public class AlleleBalance implements InfoFieldAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java index 51d290763..a99f87a70 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -1,12 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.annotator; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.gatk.contexts.*; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java index 51b5381dc..6c14e7445 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java @@ -1,8 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.variantcontext.Genotype; + import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java index 244627154..66416ce11 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java @@ -31,19 +31,19 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; public class BaseCounts implements InfoFieldAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index ff916bedd..2a5c996f7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -1,16 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import java.util.Arrays; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.List; -import java.util.Arrays; public class BaseQualityRankSumTest extends RankSumTest { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index f3ec2b1df..74f7f9d80 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -25,18 +25,22 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import java.util.*; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index e56825dbe..c384e0d09 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -1,18 +1,19 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index ee66b50ee..e3e8bc258 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -1,21 +1,20 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 2115526a6..97ed221e7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -24,20 +24,20 @@ package org.broadinstitute.sting.gatk.walkers.annotator; +import cern.jet.math.Arithmetic; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import cern.jet.math.Arithmetic; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 5eaa30bf3..48677bbe5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -1,18 +1,19 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; public class GCContent implements InfoFieldAnnotation, ExperimentalAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java index 3a5db2884..cca0ad4bc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java @@ -1,19 +1,20 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index bd8c51a41..b175579f1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -24,25 +24,29 @@ package org.broadinstitute.sting.gatk.walkers.annotator; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.genotype.Haplotype; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; -import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.genotype.Haplotype; -import org.broadinstitute.sting.utils.pileup.*; import java.util.*; -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation { private final static boolean DEBUG = false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java index ecebfbbd2..d86728d5e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java @@ -1,20 +1,21 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broad.tribble.util.popgen.HardyWeinbergCalculation; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation; import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; public class HardyWeinberg implements InfoFieldAnnotation, WorkInProgressAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index 099780fa7..02efd854c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -1,19 +1,19 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java index ee8b01d7d..12b48473d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java @@ -1,14 +1,14 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.IndelUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java index f23433bb5..1d999c531 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java @@ -1,19 +1,19 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; public class LowMQ implements InfoFieldAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index 8260a5a81..cc62580a9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -1,17 +1,17 @@ package org.broadinstitute.sting.gatk.walkers.annotator; +import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import java.util.Arrays; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.List; -import java.util.Arrays; public class MappingQualityRankSumTest extends RankSumTest { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 25a7b286d..f240d02bc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -1,16 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java index 00cc30309..0ca53adf2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java @@ -25,22 +25,22 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java index dc4934ade..08a25a7e3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java @@ -1,15 +1,15 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java index 3b64abfff..1c70a1b33 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java @@ -1,14 +1,14 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index 720984835..2175d39e6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -1,19 +1,19 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; public class QualByDepth extends AnnotationByDepth implements InfoFieldAnnotation, StandardAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index 1ef7ccd0b..d52f07b58 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -1,20 +1,23 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index f00abd6a1..5466828f6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -1,22 +1,23 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.MannWhitneyU; +import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.List; import java.util.ArrayList; -import java.util.Map; import java.util.HashMap; +import java.util.List; +import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java index a670532af..c56e2622d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java @@ -26,25 +26,24 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; -import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; +import java.util.Arrays; import java.util.HashMap; import java.util.List; -import java.util.Arrays; +import java.util.Map; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 727904a3b..aabfb2970 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -1,14 +1,17 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import net.sf.samtools.Cigar; +import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import net.sf.samtools.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java index fc769ac54..a5ebd8db2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java index e2fd2a3d4..ff9092a71 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java @@ -25,15 +25,15 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index 0b6cbcc2e..a4668eeb6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -1,14 +1,14 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java index 351117809..b46d82d8b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java @@ -5,7 +5,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.IndelUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -13,7 +12,10 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index cd5b6694b..acbeee3b2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -25,24 +25,23 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.classloader.PluginManager; +import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 54c8be73a..fdf498a3d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -25,30 +25,27 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import java.util.ArrayList; -import java.util.Collection; -import java.util.Collections; -import java.util.HashMap; -import java.util.HashSet; -import java.util.LinkedHashMap; -import java.util.LinkedList; -import java.util.List; -import java.util.Map; -import java.util.Set; -import java.util.Map.Entry; - -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; -import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*; +import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.GenomicAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.JoinTable; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.*; +import java.util.Map.Entry; public class VariantAnnotatorEngine { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java index e02c62baf..05c1b3c52 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java @@ -25,13 +25,6 @@ package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; -import java.util.*; -import java.util.Map.Entry; - -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -39,7 +32,14 @@ import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTa import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.*; +import java.util.Map.Entry; /** * This plugin for {@link VariantAnnotatorEngine} serves as the core diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java index 69a35a584..b42310780 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java @@ -26,28 +26,28 @@ package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; -import java.io.File; -import java.io.IOException; -import java.util.*; -import java.util.Map.Entry; - -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableCodec; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.io.File; +import java.io.IOException; +import java.util.*; +import java.util.Map.Entry; /** * Annotates variant calls with information from user-specified tabular files. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java index c57aacb5b..714f374cf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java @@ -25,6 +25,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; + import java.io.BufferedReader; import java.io.File; import java.io.FileReader; @@ -33,9 +36,6 @@ import java.util.ArrayList; import java.util.HashMap; import java.util.List; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; - /** * This is a container that holds all data corresponding to a single join table as specified by one -J arg (ex: -J bindingName1,/path/to/file,bindingName1.columnName=bindingName2.columnName2). * Some terminology: diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java index d3fcfd42a..3b6c87f90 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java @@ -25,16 +25,16 @@ package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; + import java.io.BufferedReader; import java.io.IOException; import java.util.ArrayList; import java.util.Collections; import java.util.List; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.exceptions.UserException; - /** * Used to parse files passed to the GenomicAnnotator via the -J arg. * The files must be tab-delimited, and the first non-empty/non-commented line diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java index 0ed61fc48..0bbfa51b4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java @@ -24,9 +24,6 @@ package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; -import java.io.*; -import java.util.*; - import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -36,17 +33,15 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableCodec; import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.gatk.walkers.By; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.RMD; -import org.broadinstitute.sting.gatk.walkers.Reference; -import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.Window; +import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import java.io.IOException; +import java.io.PrintStream; +import java.util.*; + /** * Takes a table of transcripts (eg. UCSC refGene, knownGene, and CCDS tables) and generates the big table which contains * annotations for each possible variant at each transcript position (eg. 4 variants at each genomic position). diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java index 29b256479..57bc44ab8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -1,14 +1,14 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import java.util.Map; import java.util.List; +import java.util.Map; public interface GenotypeAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java index 5b33395b5..4e850d01b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Map; import java.util.List; +import java.util.Map; public interface InfoFieldAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java index aa23abc67..21c8ec430 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java @@ -25,26 +25,26 @@ package org.broadinstitute.sting.gatk.walkers.beagle; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; + import static java.lang.Math.log10; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 93ee0b085..3eed12992 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -25,10 +25,6 @@ package org.broadinstitute.sting.gatk.walkers.beagle; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Input; @@ -36,17 +32,20 @@ import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.File; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java index 18aa3e257..f6cd1d636 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java @@ -25,28 +25,29 @@ package org.broadinstitute.sting.gatk.walkers.beagle; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.PrintStream; -import java.util.*; +import java.util.Arrays; +import java.util.Set; /** * Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java index 2c67265d6..90e6fcd77 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java @@ -22,6 +22,8 @@ package org.broadinstitute.sting.gatk.walkers.coverage; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -31,12 +33,10 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; import java.io.File; -import java.io.PrintStream; import java.io.FileNotFoundException; +import java.io.PrintStream; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java index ae947eac1..405a44c29 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java @@ -26,12 +26,11 @@ package org.broadinstitute.sting.gatk.walkers.coverage; import net.sf.samtools.SAMRecord; - -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java index 5a9c62b7f..6b91b0198 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java @@ -22,19 +22,19 @@ package org.broadinstitute.sting.gatk.walkers.coverage; +import org.broad.tribble.bed.FullBEDFeature; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broad.tribble.bed.FullBEDFeature; import org.broadinstitute.sting.utils.exceptions.UserException; -import java.util.*; import java.io.PrintStream; +import java.util.Arrays; +import java.util.List; /** * Test routine for new VariantContext object diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java index 298aa90b9..a41e55166 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java @@ -8,7 +8,9 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; -import java.util.*; +import java.util.Collection; +import java.util.HashMap; +import java.util.Map; /** * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 91ae81cd5..c1956f1d7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -26,6 +26,8 @@ package org.broadinstitute.sting.gatk.walkers.coverage; import net.sf.samtools.SAMReadGroupRecord; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -34,12 +36,13 @@ import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder; -import org.broadinstitute.sting.gatk.refdata.utils.*; +import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; +import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; +import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java index a5ebf27bb..15b16ca6b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java @@ -24,22 +24,15 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; -import net.sf.samtools.*; +import net.sf.samtools.SAMFileReader; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMRecordIterator; import net.sf.samtools.util.BlockCompressedInputStream; -import org.broad.tribble.readers.AsciiLineReader; -import org.broad.tribble.readers.LineReader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.io.DataInputStream; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.util.Arrays; -import java.util.Map; -import java.util.zip.GZIPInputStream; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java index 4c3f7bd95..eb8a71c2c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java @@ -24,7 +24,9 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; -import com.google.java.contract.*; +import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; +import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java index 3750496a1..963191446 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java @@ -24,8 +24,6 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; -import org.broadinstitute.sting.utils.Utils; - /** * Created by IntelliJ IDEA. * User: depristo diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java index a812babaf..4e44578c7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java @@ -30,7 +30,10 @@ import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.io.*; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileReader; +import java.io.IOException; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index 828d39717..efc101618 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.gatk.walkers.fasta; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Collection; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java index 6be2336c0..2dbfc76ff 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java @@ -25,16 +25,15 @@ package org.broadinstitute.sting.gatk.walkers.fasta; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.gatk.walkers.WalkerName; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java index b31526987..2c009f7f2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.filters; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; public class ClusteredSnps { private GenomeLocParser genomeLocParser; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java index c3849e240..ede19746a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.filters; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; public class FiltrationContext { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java index 225cdecc3..d7c0dd4d5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java @@ -27,7 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.*; +import java.util.LinkedList; +import java.util.List; +import java.util.ListIterator; /** * A window of variants surrounding the current variant being investigated diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 884d0ac24..6c023573a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -25,21 +25,20 @@ package org.broadinstitute.sting.gatk.walkers.filters; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java index 47be7e6fe..83a8ce7d7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java @@ -26,14 +26,15 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.PrintStream; -import java.util.*; +import java.util.Map; +import java.util.Set; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java index 22c9dcf91..696a74de8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java @@ -4,8 +4,6 @@ import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.genotype.DiploidGenotype; -import java.util.Arrays; - /** * Created by IntelliJ IDEA. * User: delangel diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java index ab075eaf2..2014801e4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java @@ -26,13 +26,14 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import net.sf.samtools.SAMUtils; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.pileup.FragmentPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.genotype.DiploidGenotype; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.sting.utils.pileup.FragmentPileup; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import static java.lang.Math.log10; import static java.lang.Math.pow; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java index 89504b371..5c27bc943 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java @@ -26,17 +26,22 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.SimpleTimer; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.exceptions.UserException; import sun.reflect.generics.reflectiveObjects.NotImplementedException; -import java.util.*; import java.io.PrintStream; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Map; +import java.util.Set; public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel { // diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index 3902a0b7f..8261cd588 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -30,11 +30,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Allele; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java index c4e315f68..10b646d63 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java @@ -26,18 +26,18 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; import java.io.PrintStream; +import java.util.*; public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 1f430548b..be2039780 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -25,16 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.genotype.Haplotype; @@ -42,11 +40,10 @@ import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java index 2cf149fd0..3652763de 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.sting.utils.variantcontext.Allele; import java.util.ArrayList; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 9f4d4182f..3e3cd128b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -25,23 +25,25 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.genotype.DiploidGenotype; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java index cf1c57a05..22c3081a3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java @@ -25,8 +25,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.DownsampleType; @@ -36,8 +34,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.HashSet; +import java.util.Set; +import java.util.TreeSet; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java index 1533e8777..68d8f9b54 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java @@ -24,19 +24,19 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 055eb0b97..2b25df4aa 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.commandline.Input; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index fc8a5819a..2a0338bca 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -25,22 +25,25 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.gatk.contexts.*; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.ArgumentCollection; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.DownsampleType; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.filters.BadMateFilter; +import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.DownsampleType; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.utils.codecs.vcf.*; -import java.util.*; import java.io.PrintStream; +import java.util.*; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 6fc972b5d..a10897172 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -25,22 +25,24 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; +import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import com.google.java.contract.*; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.PrintStream; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java index df1f4f908..adb7c4c38 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java @@ -1,11 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.indels; import net.sf.picard.sam.SamPairUtil; -import net.sf.samtools.*; +import net.sf.samtools.SAMFileWriter; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMRecordComparator; +import net.sf.samtools.SAMRecordCoordinateComparator; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java index 7617aa9de..e68aa31e0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java @@ -25,21 +25,16 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.AlignmentBlock; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.genotype.Haplotype; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; import java.util.Arrays; import java.util.HashMap; -import java.util.List; public class HaplotypeIndelErrorModel { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index a53665d64..61f21c488 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -25,39 +25,41 @@ package org.broadinstitute.sting.gatk.walkers.indels; +import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.*; import net.sf.samtools.util.RuntimeIOException; -import net.sf.samtools.util.StringUtil; import net.sf.samtools.util.SequenceUtil; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.commandline.*; +import net.sf.samtools.util.StringUtil; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.walkers.BAQMode; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; +import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; +import org.broadinstitute.sting.gatk.walkers.BAQMode; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator; +import org.broadinstitute.sting.utils.interval.IntervalMergingRule; +import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.NwayIntervalMergingIterator; +import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter; +import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java index 010e0cf6f..af8051334 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java @@ -25,8 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.*; -import org.broadinstitute.sting.commandline.*; +import net.sf.samtools.Cigar; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index ab7ae4184..60262d6f4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -28,30 +28,25 @@ package org.broadinstitute.sting.gatk.walkers.indels; import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -/*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate; -import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager; -import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum; -import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection; -*/import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.collections.NestedHashMap; -import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.genotype.Haplotype; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.sting.utils.variantcontext.Allele; import java.io.File; -import java.io.FileNotFoundException; -import java.util.*; -import java.util.regex.Pattern; +import java.util.Arrays; +import java.util.HashMap; +import java.util.LinkedHashMap; + +/*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate; +import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager; +import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum; +import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection; +*/ public class PairHMMIndelErrorModel { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java index fc196e712..2c89b907b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java @@ -25,19 +25,23 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.*; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.filters.BadMateFilter; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator; -import org.broadinstitute.sting.utils.sam.ReadUtils; +import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.filters.BadMateFilter; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.By; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator; +import org.broadinstitute.sting.utils.interval.IntervalMergingRule; +import org.broadinstitute.sting.utils.sam.ReadUtils; import java.io.File; -import java.util.*; +import java.util.Iterator; @By(DataSource.READS) // walker to count realigned reads diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index 3b94989aa..488e37f26 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -25,27 +25,27 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.filters.BadCigarFilter; -import org.broadinstitute.sting.gatk.filters.Platform454Filter; -import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter; import org.broadinstitute.sting.gatk.filters.BadMateFilter; +import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter; +import org.broadinstitute.sting.gatk.filters.Platform454Filter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.ArrayList; import java.io.PrintStream; +import java.util.ArrayList; /** * Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java index 1fe3fdd04..3854a4a8c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java @@ -23,7 +23,8 @@ */ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.*; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMRecordCoordinateComparator; /** * Extends Picard's Comparator for sorting SAMRecords by coordinate. This one actually deals with unmapped reads diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java index 1f05ddaf0..443e6e9f2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java @@ -25,15 +25,21 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import net.sf.samtools.*; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Tags; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; -import org.broadinstitute.sting.gatk.filters.*; -import org.broadinstitute.sting.gatk.refdata.*; +import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter; +import org.broadinstitute.sting.gatk.filters.Platform454Filter; +import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter; +import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator; +import org.broadinstitute.sting.gatk.refdata.Transcript; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; @@ -42,22 +48,22 @@ import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODItera import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.walkers.ReadFilters; import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.collections.CircularArray; import org.broadinstitute.sting.utils.collections.PrimitivePair; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.Hidden; - -import net.sf.samtools.*; +import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator; +import org.broadinstitute.sting.utils.interval.IntervalMergingRule; +import org.broadinstitute.sting.utils.interval.IntervalUtils; +import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator; +import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java index 869edf784..cb123c868 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java @@ -23,9 +23,9 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java index 81d9b4ddb..9aa370d3f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java @@ -24,14 +24,10 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature; @@ -41,9 +37,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.AminoAci import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java index 709bc44ce..5bd438605 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java @@ -24,10 +24,6 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -35,7 +31,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java index abced442e..b0491a281 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java @@ -24,20 +24,19 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequenceFile; import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java index ec6f5c648..be15d4541 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java @@ -24,20 +24,22 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java index fbe6e5b5a..9702fd18c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java @@ -23,27 +23,28 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.DisjointSet; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.HasGenomeLocation; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java index db1f888a1..153c4a23f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java @@ -23,10 +23,10 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; public class SNPallelePair extends AllelePair { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java index f82e48abd..2851ace0d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java @@ -24,9 +24,9 @@ package org.broadinstitute.sting.gatk.walkers.phasing; import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; public class WriteVCF { public static void writeVCF(VariantContext vc, VCFWriter writer, Logger logger) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java index feb5f62af..2bdd4558f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java @@ -6,14 +6,12 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.RefWalker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; -import java.util.List; import java.io.PrintStream; +import java.util.List; /** * Counts the number of contiguous regions the walker traverses over. Slower than it needs to be, but diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java index ef6ff04f2..0d68c8493 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import net.sf.samtools.SAMFileWriter; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java index cece04fcf..df89efe6d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java @@ -25,14 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.qc; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.walkers.ReadPairWalker; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; -import org.broadinstitute.sting.commandline.Output; -import net.sf.samtools.SAMRecord; +import java.io.PrintStream; import java.util.Collection; import java.util.List; -import java.io.PrintStream; /** * Counts the number of read pairs encountered in a file sorted in diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java index 74f63aa2f..87c0409b9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java @@ -1,11 +1,11 @@ package org.broadinstitute.sting.gatk.walkers.qc; import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.walkers.Requires; /** * Walks over the input data set, calculating the number of reads seen for diagnostic purposes. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java index a4e80138f..d1545f159 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.gatk.walkers.qc; +import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.commandline.Argument; /** * Prints out counts of the number of reference ordered data objects are diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java index 92867e1a9..8a03dea44 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java @@ -27,23 +27,24 @@ package org.broadinstitute.sting.gatk.walkers.qc; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; +import java.io.PrintStream; import java.util.ArrayList; -import java.util.List; import java.util.Collection; import java.util.LinkedList; -import java.io.PrintStream; +import java.util.List; /** * Prints out counts of the number of reference ordered data objects are diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java index 5ae35416a..b5f5442cd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java @@ -25,22 +25,22 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.collections.PrimitivePair; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import net.sf.samtools.SAMReadGroupRecord; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMReadGroupRecord; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.utils.collections.PrimitivePair; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import java.util.*; import java.io.*; +import java.util.*; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java index 39b69ba29..d3b992cb5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java @@ -1,16 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.qc; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import java.util.List; -import java.util.Arrays; import java.io.PrintStream; - -import net.sf.samtools.SAMRecord; +import java.util.Arrays; +import java.util.List; /** * At each locus in the input data set, prints the reference base, genomic location, and diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java index 2f1773d01..908e389a8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java @@ -22,21 +22,24 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; +import net.sf.samtools.SAMReadGroupRecord; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import net.sf.samtools.*; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import java.util.*; -import java.io.*; +import java.io.PrintStream; +import java.util.Arrays; /** * User: depristo diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java index 6ad0340a4..fa1bb4d55 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java @@ -1,16 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.qc; +import net.sf.samtools.SAMFileWriter; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMFileWriter; import java.security.MessageDigest; import java.security.NoSuchAlgorithmException; -import java.util.List; import java.util.ArrayList; +import java.util.List; /* diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java index 9cb715507..170630b77 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -8,8 +7,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.gatk.walkers.Reference; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.*; import java.math.BigInteger; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java index bc68be592..e1e6c4b69 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java @@ -25,20 +25,20 @@ package org.broadinstitute.sting.gatk.walkers.qc; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import java.util.Arrays; import java.io.PrintStream; +import java.util.Arrays; /** * At every locus in the input set, compares the pileup data (reference base, aligned base from diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java index 568e1b638..fc6b3daee 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java @@ -7,7 +7,6 @@ import org.broadinstitute.sting.utils.text.XReadLines; import java.io.File; import java.io.FileNotFoundException; import java.io.PrintStream; -import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.regex.Pattern; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java index c21f548b3..8c6539f8d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java @@ -27,24 +27,25 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; import org.broad.tribble.bed.BEDCodec; import org.broad.tribble.dbsnp.DbSNPCodec; -import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter; -import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Gather; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter; import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; +import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.utils.collections.NestedHashMap; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java index 64e0864c0..945d02837 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java @@ -1,7 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; import net.sf.samtools.SAMRecord; - import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java index 0de6897d0..a7717161a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java @@ -1,11 +1,10 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import java.util.HashMap; - import net.sf.samtools.SAMRecord; - import org.broadinstitute.sting.utils.BaseUtils; +import java.util.HashMap; + /* * Copyright (c) 2009 The Broad Institute * diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java index fdbeb6a31..e6d0b306c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java @@ -25,19 +25,21 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; +import net.sf.samtools.SAMReadGroupRecord; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMUtils; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.collections.NestedHashMap; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.collections.NestedHashMap; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import java.util.*; - -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMUtils; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java index 7ba441ccc..f04989fa5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.QualityUtils; -import java.util.*; +import java.util.List; /* * Copyright (c) 2010 The Broad Institute diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java index 0eaa1245e..0277fda0d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java @@ -25,31 +25,33 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import java.io.File; -import java.io.FileNotFoundException; -import java.util.*; -import java.util.regex.Pattern; - import net.sf.samtools.*; import net.sf.samtools.util.SequenceUtil; - +import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.collections.NestedHashMap; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.utils.classloader.PluginManager; +import org.broadinstitute.sting.utils.collections.NestedHashMap; +import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.text.TextFormattingUtils; +import org.broadinstitute.sting.utils.text.XReadLines; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.ArrayList; +import java.util.List; +import java.util.MissingResourceException; +import java.util.ResourceBundle; +import java.util.regex.Pattern; /** * This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java index c1c17bda5..b3b63bb96 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java @@ -1,12 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.sequenom; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java index fde233b5d..b877ff70b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java @@ -25,29 +25,27 @@ package org.broadinstitute.sting.gatk.walkers.sequenom; -import net.sf.samtools.util.CloseableIterator; import org.broad.tribble.bed.BEDCodec; -import org.broad.tribble.dbsnp.DbSNPCodec; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.*; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; +import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; -import java.util.*; import java.io.PrintStream; +import java.util.*; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index c9c5e09a8..fe3173506 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -1,14 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; +import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; @@ -20,22 +18,21 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.*; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.io.FileNotFoundException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.File; +import java.io.FileNotFoundException; import java.io.PrintStream; import java.lang.reflect.Field; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java index 787dbe9af..925bff9c0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.variantcontext.Genotype; class NewCompEvalGenotypes { private GenomeLoc loc; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index 85373baa8..255a54737 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -1,12 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; /** * The Broad Institute diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index befb2ff13..8c281b2f8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; @Analysis(description = "Counts different classes of variants in the sample") public class CountVariants extends VariantEvaluator implements StandardEval { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java index 58803c9d0..bbd3f5f54 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java @@ -1,18 +1,18 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java index 407b71893..a476a2680 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java @@ -1,9 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.*; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -12,8 +9,12 @@ import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.HashMap; import java.util.HashSet; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index f7f9fce0c..77def0f30 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; /** * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java index dd4bb492e..6e1b76acd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java @@ -1,14 +1,14 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java index 1bd420e0a..d99196ecf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java @@ -1,15 +1,15 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.IndelUtils; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 16ec74433..a0cc393d9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -1,15 +1,15 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.MendelianViolation; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; /** * Mendelian violation detection and counting diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java index e83914ef8..b209ee13d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java @@ -24,12 +24,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites") public class PrintMissingComp extends VariantEvaluator { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java index 5f3e6b0fa..751f61a97 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.variantcontext.Genotype; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java index 395309975..d466645ea 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java @@ -1,17 +1,18 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.*; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.ArrayList; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index f9cda5e0b..ec43cbd55 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index deeafd851..be957abd7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -1,13 +1,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; @Analysis(description = "Ti/Tv Variant Evaluator") public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index 756427581..9c331b577 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -1,16 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Set; /** * The Broad Institute diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java index 6017ecca3..e29e7ed50 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java @@ -1,12 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext; import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; public abstract class VariantEvaluator { public void initialize(VariantEvalWalker walker) {} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java index 29a61e27a..b6ad55b18 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java @@ -25,16 +25,16 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.ArrayList; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java index 2cbc66e31..411493d4f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -1,12 +1,11 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; -import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java index 48b4ffa91..2ffc7716c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java @@ -1,10 +1,10 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java index 9942ba8d6..c6975808f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java index 1a9d31085..c14355035 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java index 15b1d41c1..3e8a6ed17 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java index 65af6090c..155a66186 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java @@ -1,14 +1,14 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.HashMap; -import java.util.Set; import java.util.HashSet; +import java.util.Set; public class Degeneracy extends VariantStratifier { private ArrayList states; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java index 7bd15a974..40f952fd2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java index 8d8782ab7..3b7a419f2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java index fd724d6d1..c6c094f8e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java index a7ccd3182..76efedbf4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java @@ -1,10 +1,10 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java index 39d2e6b4d..a0973a088 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Collection; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java index f909de4f3..a2a3eb3fb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java index 218cb23ca..2c4b8bc46 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java @@ -1,11 +1,10 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java index 3208c26bb..8112ae97f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -9,6 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvalu import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.HashMap; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java index 0281653af..38f7a7f40 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; -import org.apache.commons.jexl2.*; +import org.apache.commons.jexl2.Expression; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index eabd2e588..0a915db37 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -1,9 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; @@ -16,6 +14,8 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Variant import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.lang.reflect.Field; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index d4e07dccf..403c67d3e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -25,23 +25,23 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.collections.NestedHashMap; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; import java.io.FileNotFoundException; -import java.lang.Double; import java.util.*; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java index 64fe36637..15424f0f7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java @@ -25,11 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; -import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; -import java.io.*; +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileNotFoundException; +import java.io.PrintStream; import java.util.*; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java index 5deb5d8c2..bc7252ec2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java @@ -26,10 +26,10 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index ddeda1699..67d54a408 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -34,9 +33,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.PrintStream; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 2d0355d7d..8179463eb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -25,14 +25,12 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; @@ -42,6 +40,8 @@ import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 597a54dc1..837f352f8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Requires; @@ -38,11 +38,10 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index ba6f5e513..b45ee1b67 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -24,18 +24,21 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Arrays; +import java.util.Collection; +import java.util.Map; +import java.util.Set; /** * Filters a lifted-over VCF file for ref bases that have been changed. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index d9dd85f0c..2ebd183f4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -28,21 +28,17 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 7eda54387..4f05c8aac 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -24,27 +24,27 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; - -import java.io.File; -import java.util.*; - import net.sf.picard.PicardException; import net.sf.picard.liftover.LiftOver; import net.sf.picard.util.Interval; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileReader; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RMD; +import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; + +import java.io.File; +import java.util.*; /** * Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java index 0c41a9728..f0756d884 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java @@ -24,11 +24,6 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; @@ -39,11 +34,15 @@ import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashSet; +import java.util.Set; /** * Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index cbac54326..1db692e9f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -24,27 +24,26 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.MendelianViolation; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.MendelianViolation; import org.broadinstitute.sting.utils.SampleUtils; -import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.File; -import java.lang.annotation.AnnotationFormatError; import java.util.*; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index 1bd73414c..0644c669b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -25,22 +25,25 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broad.tribble.dbsnp.DbSNPFeature; import org.broad.tribble.TribbleException; +import org.broad.tribble.dbsnp.DbSNPFeature; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; import java.io.File; +import java.util.Collection; +import java.util.HashSet; +import java.util.List; +import java.util.Set; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index 482679593..86bb3b0e8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -25,20 +25,19 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 71dd5df3f..8d90af65a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -24,18 +24,17 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.PrintStream; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 79134b553..aa0e5987f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -28,26 +28,26 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import net.sf.samtools.util.CloseableIterator; import org.broad.tribble.dbsnp.DbSNPCodec; import org.broad.tribble.dbsnp.DbSNPFeature; -import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature; +import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java b/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java index b01533ee6..b5efcc153 100644 --- a/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java +++ b/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java @@ -24,7 +24,10 @@ package org.broadinstitute.sting.jna.clibrary; -import com.sun.jna.*; +import com.sun.jna.LastErrorException; +import com.sun.jna.Native; +import com.sun.jna.NativeLong; +import com.sun.jna.Structure; import com.sun.jna.ptr.NativeLongByReference; /** diff --git a/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java b/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java index 0c0579d6f..c7b3de6cf 100644 --- a/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java +++ b/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java @@ -29,7 +29,7 @@ import com.sun.jna.ptr.FloatByReference; import com.sun.jna.ptr.IntByReference; import com.sun.jna.ptr.PointerByReference; import org.broadinstitute.sting.jna.clibrary.JNAUtils; -import org.broadinstitute.sting.jna.clibrary.LibC.*; +import org.broadinstitute.sting.jna.clibrary.LibC.timeval; /* NOTE: This library uses Pointer for some Struct.ByReference members going diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java index fe6758e76..c09c4037e 100644 --- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java @@ -27,13 +27,16 @@ package org.broadinstitute.sting.queue.extensions.gatk; import net.sf.samtools.BAMIndex; import net.sf.samtools.SAMFileWriter; import org.broad.tribble.Tribble; -import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import java.io.File; import java.lang.annotation.Annotation; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; public abstract class ArgumentDefinitionField extends ArgumentField { diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java index 2da427d44..e90933504 100644 --- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java +++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java @@ -35,7 +35,10 @@ import java.io.File; import java.io.InputStream; import java.io.OutputStream; import java.lang.annotation.Annotation; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; public abstract class ArgumentField { diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java index 21fb44733..5095bd6e5 100644 --- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java +++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java @@ -27,17 +27,20 @@ package org.broadinstitute.sting.queue.extensions.gatk; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor; +import org.broadinstitute.sting.commandline.CommandLineProgram; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.commandline.ParsingEngine; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.WalkerManager; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.filters.FilterManager; import org.broadinstitute.sting.gatk.filters.ReadFilter; -import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; +import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder; import org.broadinstitute.sting.gatk.walkers.PartitionBy; import org.broadinstitute.sting.gatk.walkers.PartitionType; diff --git a/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java b/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java index 5f68d3414..52c18e6d6 100644 --- a/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java +++ b/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java @@ -23,7 +23,9 @@ */ package org.broadinstitute.sting.utils; -import java.util.*; +import java.util.Collection; +import java.util.Set; +import java.util.TreeSet; public class DisjointSet { private ItemNode[] nodes; diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index 1f8800542..b96923589 100644 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.Serializable; diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 18a1e7ffd..a5c6e0537 100644 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -25,12 +25,14 @@ package org.broadinstitute.sting.utils; -import com.google.java.contract.*; +import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; +import com.google.java.contract.Requires; +import com.google.java.contract.ThrowEnsures; import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; - import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java index 30e1a3f5b..af69ebca6 100755 --- a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.utils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java index 50aa0f707..36ed506aa 100755 --- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java @@ -25,17 +25,14 @@ package org.broadinstitute.sting.utils; -import cern.jet.math.Arithmetic; - -import java.math.BigDecimal; -import java.util.*; - import com.google.java.contract.Requires; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.utils.exceptions.UserException; +import java.math.BigDecimal; +import java.util.*; + /** * MathUtils is a static class (no instantiation allowed!) with some useful math methods. * diff --git a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java index a8089ffe8..c6a07b5ce 100755 --- a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java +++ b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java @@ -1,12 +1,13 @@ package org.broadinstitute.sting.utils; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Collection; +import java.util.List; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/public/java/src/org/broadinstitute/sting/utils/PathUtils.java b/public/java/src/org/broadinstitute/sting/utils/PathUtils.java index 47466be20..822d04dfd 100755 --- a/public/java/src/org/broadinstitute/sting/utils/PathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/PathUtils.java @@ -2,10 +2,10 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.List; -import java.util.ArrayList; import java.io.File; import java.io.FilenameFilter; +import java.util.ArrayList; +import java.util.List; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java b/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java index 30257d967..a758df431 100644 --- a/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java +++ b/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java @@ -3,7 +3,9 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Iterator; /** * Randomly downsample from a stream of elements. This algorithm is a direct, diff --git a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java index 4b7fa3e41..92d73a5ce 100755 --- a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java +++ b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java @@ -24,15 +24,14 @@ package org.broadinstitute.sting.utils; +import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import net.sf.samtools.Cigar; - -import java.util.*; - import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.StingException; +import java.util.*; + /** * Created by IntelliJ IDEA. * User: asivache diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java index c0370064d..f9997bfd8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java @@ -27,12 +27,12 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java b/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java index a59c5134a..342087b41 100644 --- a/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java +++ b/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java @@ -1,7 +1,10 @@ package org.broadinstitute.sting.utils; +import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; +import com.google.java.contract.Requires; + import java.io.PrintStream; -import com.google.java.contract.*; /** * A useful simple system for timing code. This code is not thread safe! diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java index 4c13d8b18..6a50badce 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java @@ -25,13 +25,12 @@ package org.broadinstitute.sting.utils; -import java.util.*; - import net.sf.samtools.util.StringUtil; - import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.collections.Pair; +import java.util.*; + /** * Created by IntelliJ IDEA. * User: depristo diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java index 456f0fa0f..ef7cf751e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java @@ -1,10 +1,10 @@ package org.broadinstitute.sting.utils.baq; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequence; +import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java index 24d4152a5..26356a4a4 100644 --- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java @@ -2,11 +2,10 @@ package org.broadinstitute.sting.utils.baq; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMRecord; import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.Iterator; diff --git a/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java b/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java index abcae066f..b95165841 100644 --- a/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java +++ b/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java @@ -1,11 +1,12 @@ package org.broadinstitute.sting.utils.bed; -import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.*; -import java.util.*; +import java.util.ArrayList; +import java.util.List; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java index 404bd80b6..e65b8f921 100755 --- a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java @@ -29,9 +29,9 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.reflections.util.ClasspathHelper; -import java.lang.reflect.*; import java.io.File; import java.io.IOException; +import java.lang.reflect.*; import java.net.URL; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java index 95f3e160c..5449906b2 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java @@ -4,9 +4,6 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.walkers.ClipReadsWalker; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ReadUtils; import java.util.Vector; diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java index 031467ed9..988d297f6 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java @@ -1,7 +1,6 @@ package org.broadinstitute.sting.utils.clipreads; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.walkers.ClipReadsWalker; import java.util.ArrayList; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java index a286ce789..fef6c4ea0 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java @@ -30,7 +30,6 @@ import org.broad.tribble.readers.LineReader; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.io.IOException; import java.util.HashMap; import java.util.HashSet; import java.util.regex.Matcher; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java index 618d9ce79..e169dbdfc 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java @@ -4,11 +4,11 @@ import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; import org.broad.tribble.NameAwareCodec; import org.broad.tribble.TribbleException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.readers.LineReader; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java index e7ddac185..b7f4be39a 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java @@ -33,13 +33,13 @@ import org.broad.tribble.util.LittleEndianOutputStream; import org.broad.tribble.util.ParsingUtils; import org.broad.tribble.util.PositionalStream; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.*; -import java.util.*; import java.lang.reflect.Array; +import java.util.*; /** * this class writes VCF files diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java index dac996494..1dba351e2 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java @@ -2,7 +2,9 @@ package org.broadinstitute.sting.utils.codecs.vcf; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; -import java.util.*; + +import java.util.List; +import java.util.Map; /** diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java index 4037f75b9..f43891e77 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.codecs.vcf; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java b/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java index a36ed9ac6..d280ac804 100755 --- a/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java +++ b/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java @@ -25,7 +25,8 @@ package org.broadinstitute.sting.utils.collections; -import java.util.*; +import java.util.HashMap; +import java.util.Map; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java index 3a731c2fd..6d6cb8272 100644 --- a/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java @@ -27,10 +27,13 @@ package org.broadinstitute.sting.utils.collections; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.*; +import java.util.Collection; +import java.util.Iterator; +import java.util.LinkedList; +import java.util.PriorityQueue; public class RODMergingIterator implements Iterator, Iterable { PriorityQueue queue = new PriorityQueue(); diff --git a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java index 41de5ef96..bba47c76c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java @@ -26,15 +26,18 @@ package org.broadinstitute.sting.utils.duplicates; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import java.util.List; import java.util.Arrays; +import java.util.List; public class DupUtils { private static SAMRecord tmpCopyRead(SAMRecord read) { diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 17c4a7df4..7eab6f6c9 100755 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -28,9 +28,8 @@ import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.File; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java index 0c5085cc7..43ef4aa74 100644 --- a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java +++ b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java @@ -25,15 +25,16 @@ package org.broadinstitute.sting.utils.fasta; import net.sf.picard.PicardException; -import net.sf.picard.reference.*; +import net.sf.picard.reference.FastaSequenceIndex; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.picard.reference.ReferenceSequence; import net.sf.samtools.SAMSequenceRecord; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; import java.io.FileNotFoundException; import java.util.Arrays; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - /** * A caching version of the IndexedFastaSequenceFile that avoids going to disk as often as the raw indexer. * diff --git a/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java index cbfba848c..1c2cfe2e1 100755 --- a/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java @@ -26,7 +26,6 @@ package org.broadinstitute.sting.utils.genotype; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.MathUtils; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java index 31791e805..a17e81461 100755 --- a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java @@ -24,14 +24,14 @@ package org.broadinstitute.sting.utils.genotype; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variantcontext.Allele; -import java.util.*; +import java.util.Arrays; +import java.util.LinkedHashMap; +import java.util.List; public class Haplotype { protected byte[] bases = null; diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java index d9e74640f..483c874dc 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.utils.help; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.commandline.CommandLineProgram; +import org.broadinstitute.sting.utils.classloader.JVMUtils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.List; -import java.util.Collections; import java.io.IOException; +import java.util.Collections; +import java.util.List; /** * Contains details additional details that the program can diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java index 68633a2b3..65c332048 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java @@ -1,7 +1,6 @@ package org.broadinstitute.sting.utils.help; import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.Tag; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java index be6f7f3eb..6c6dad736 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java @@ -1,7 +1,6 @@ package org.broadinstitute.sting.utils.help; import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.Tag; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java index 493f26e76..a9d71ef98 100755 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java @@ -25,22 +25,16 @@ package org.broadinstitute.sting.utils.help; +import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.ArgumentDefinition; import org.broadinstitute.sting.commandline.ArgumentDefinitionGroup; import org.broadinstitute.sting.commandline.ArgumentDefinitions; -import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.Utils; -import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.text.TextFormattingUtils; -import java.util.Formatter; -import java.util.List; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.Comparator; -import java.util.Collection; -import java.util.Collections; import java.text.DateFormat; import java.text.SimpleDateFormat; +import java.util.*; /** * Print out help for Sting command-line applications. */ diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java index b962664eb..b350b1a29 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java @@ -1,9 +1,7 @@ package org.broadinstitute.sting.utils.help; -import com.sun.tools.doclets.Taglet; import com.sun.javadoc.Tag; - -import java.util.Map; +import com.sun.tools.doclets.Taglet; /** * Basic functionality for the help taglet. diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java index 4afac69c3..6ee12d42e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java @@ -26,14 +26,16 @@ package org.broadinstitute.sting.utils.help; import com.sun.javadoc.*; +import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.classloader.JVMUtils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.*; -import java.util.*; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.classloader.JVMUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.gatk.walkers.Walker; +import java.util.HashSet; +import java.util.Properties; +import java.util.Scanner; +import java.util.Set; /** * Extracts certain types of javadoc (specifically package and class descriptions) and makes them available diff --git a/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java index 036bbec4f..db8b55940 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java @@ -1,7 +1,6 @@ package org.broadinstitute.sting.utils.help; import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.Tag; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java b/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java index 3420c9876..73a29ba4f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java +++ b/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java @@ -27,9 +27,9 @@ package org.broadinstitute.sting.utils.instrumentation; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.instrument.Instrumentation; +import java.lang.reflect.Array; import java.lang.reflect.Field; import java.lang.reflect.Modifier; -import java.lang.reflect.Array; import java.util.IdentityHashMap; /** diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java index e722ac196..988240ef9 100644 --- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java @@ -25,16 +25,16 @@ package org.broadinstitute.sting.utils.interval; +import org.broadinstitute.sting.gatk.iterators.PushbackIterator; +import org.broadinstitute.sting.gatk.refdata.utils.StringToGenomeLocIteratorAdapter; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.gatk.iterators.PushbackIterator; -import org.broadinstitute.sting.gatk.refdata.utils.StringToGenomeLocIteratorAdapter; -import java.util.Iterator; import java.io.File; import java.io.FileNotFoundException; +import java.util.Iterator; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java index 80dc35455..f551e1368 100644 --- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java @@ -5,17 +5,17 @@ import net.sf.picard.util.IntervalList; import net.sf.samtools.SAMFileHeader; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.bed.BedParser; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; +import java.io.File; import java.io.IOException; import java.util.*; -import java.io.File; /** * Parse text representations of interval strings that diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java index 31a2f41fb..7e87ce8b5 100644 --- a/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java @@ -26,11 +26,10 @@ package org.broadinstitute.sting.utils.interval; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import java.util.PriorityQueue; import java.util.Iterator; +import java.util.PriorityQueue; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java index 0b63d582e..29ffb13e4 100755 --- a/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java @@ -25,9 +25,8 @@ package org.broadinstitute.sting.utils.interval; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.gatk.iterators.PushbackIterator; +import org.broadinstitute.sting.utils.GenomeLoc; import java.util.Iterator; diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java index 543302446..3821c9c8a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java @@ -24,19 +24,16 @@ package org.broadinstitute.sting.utils.pileup; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.sample.Sample; -import org.broadinstitute.sting.utils.HasGenomeLocation; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.gatk.iterators.IterableIterator; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.StingException; import java.util.*; -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.exceptions.StingException; - /** * A generic implementation of read-backed pileups. * diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java index b6f3e9f09..26e66014c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java @@ -1,8 +1,5 @@ package org.broadinstitute.sting.utils.pileup; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.BaseUtils; import net.sf.samtools.SAMRecord; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java index 6c855c1c7..f7d237401 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java @@ -1,6 +1,9 @@ package org.broadinstitute.sting.utils.pileup; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashMap; +import java.util.Map; /** * An easy to access fragment-based pileup, which contains two separate pileups. The first diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java b/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java index d8af2ea8f..7005cf869 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java @@ -27,9 +27,9 @@ package org.broadinstitute.sting.utils.pileup; import net.sf.picard.util.PeekableIterator; import org.broadinstitute.sting.gatk.datasources.sample.Sample; -import java.util.PriorityQueue; import java.util.Comparator; import java.util.Iterator; +import java.util.PriorityQueue; /** * Merges multiple pileups broken down by sample. diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java index 51e02bf74..66e1afecb 100755 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -1,9 +1,10 @@ package org.broadinstitute.sting.utils.pileup; -import org.broadinstitute.sting.utils.*; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.sam.ReadUtils; -import com.google.java.contract.*; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java index a32aa5645..8d43a368a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java @@ -24,15 +24,13 @@ package org.broadinstitute.sting.utils.pileup; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; -import java.util.Iterator; -import java.util.List; import java.util.Collection; - -import net.sf.samtools.SAMRecord; +import java.util.List; /** * A clean interface for working with extended event pileups. diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java index a1a08c95f..31d29430a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java @@ -23,15 +23,14 @@ */ package org.broadinstitute.sting.utils.pileup; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.datasources.sample.Sample; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.*; -import net.sf.samtools.SAMRecord; - public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup implements ReadBackedExtendedEventPileup { private int nInsertions; private int maxDeletionLength; // cached value of the length of the longest deletion observed at the site diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java index c52cc0b52..36b8a8c65 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java @@ -24,14 +24,13 @@ package org.broadinstitute.sting.utils.pileup; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.gatk.iterators.IterableIterator; -import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.HasGenomeLocation; -import java.util.List; import java.util.Collection; +import java.util.List; /** * A data retrieval interface for accessing parts of the pileup. diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java index 70eba577c..e5b054961 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java @@ -23,9 +23,9 @@ */ package org.broadinstitute.sting.utils.pileup; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.utils.GenomeLoc; -import net.sf.samtools.SAMRecord; import java.util.List; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 4e4294b20..344eccb83 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -25,15 +25,16 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import java.util.ArrayList; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java index 5812c9aec..5f7db458a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java @@ -1,15 +1,13 @@ package org.broadinstitute.sting.utils.sam; -import org.broadinstitute.sting.gatk.traversals.TraversalEngine; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.apache.log4j.Logger; - -import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMRecord; +import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; +import org.broadinstitute.sting.gatk.traversals.TraversalEngine; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.gatk.walkers.Walker; /* diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java index ce6ca570c..adf60b16b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java @@ -1,15 +1,17 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.*; - -import java.io.InputStream; -import java.io.ByteArrayInputStream; -import java.io.UnsupportedEncodingException; -import java.util.*; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.io.ByteArrayInputStream; +import java.io.InputStream; +import java.io.UnsupportedEncodingException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Iterator; +import java.util.List; /** * User: hanna * Date: Jun 11, 2009 diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java index b683f5247..62e371bc0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java @@ -1,9 +1,8 @@ package org.broadinstitute.sting.utils.sam; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.gatk.ReadProperties; -import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import java.util.Iterator; diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java index 4f5dcca61..2b359fe6a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java @@ -1,13 +1,12 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMSequenceRecord; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.List; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - /* * Copyright (c) 2009 The Broad Institute diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java index 01f1dfe96..31deb7535 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java @@ -26,8 +26,6 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; public class ComparableSAMRecord implements Comparable { diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java index 2b8ac387c..c7ffcab0c 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.*; +import net.sf.samtools.SAMReadGroupRecord; /** * @author ebanks diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index f3d9edab9..517f9f75d 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -1,12 +1,14 @@ package org.broadinstitute.sting.utils.sam; -import java.lang.reflect.Method; -import java.util.*; - import net.sf.samtools.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import java.lang.reflect.Method; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + /** * @author ebanks * GATKSAMRecord diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index 080762039..6c15910b1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -25,13 +25,14 @@ package org.broadinstitute.sting.utils.sam; -import com.google.java.contract.*; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; import net.sf.samtools.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.*; import java.io.File; +import java.util.*; /** * A miscellaneous collection of utilities for working with SAM files, headers, etc. diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java index f8a0ca6a7..bb9db5d98 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java @@ -26,11 +26,10 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.SAMFileReader; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - /** * Allows the user to steadily accumulate information about what * components go into a SAM file writer, ultimately using this diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java b/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java index df2010e8b..60e1d9948 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java @@ -3,13 +3,6 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.UserException; - -import java.util.Iterator; -import java.util.NoSuchElementException; /** * XXX diff --git a/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java b/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java index 9beb7895b..f6aa882ad 100644 --- a/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java @@ -26,7 +26,6 @@ package org.broadinstitute.sting.utils.text; import org.broadinstitute.sting.commandline.ParsingEngine; import org.broadinstitute.sting.commandline.Tags; -import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; diff --git a/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java index 803d6ac0f..1d4251542 100644 --- a/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java @@ -28,11 +28,11 @@ package org.broadinstitute.sting.utils.text; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.*; -import java.util.regex.Pattern; -import java.util.regex.Matcher; -import java.io.StringReader; import java.io.IOException; +import java.io.StringReader; +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; /** * Common utilities for dealing with text formatting. diff --git a/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java b/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java index 064256388..52b6f3b01 100644 --- a/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java +++ b/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.text; -import java.util.Iterator; -import java.util.List; -import java.util.LinkedList; import java.io.*; +import java.util.Iterator; +import java.util.LinkedList; +import java.util.List; /** * Support for Python-like xreadlines() function as a class. This is an iterator and iterable over diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java b/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java index cae099eeb..3763ec67d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java +++ b/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java @@ -1,18 +1,14 @@ package org.broadinstitute.sting.utils.threading; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.*; -import java.nio.ByteBuffer; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collection; import java.util.List; -import java.util.concurrent.locks.ReentrantLock; /** * Keeps a copy of the processing locks in a file diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java b/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java index 4e61ef9e1..ad2a6d31b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java +++ b/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java @@ -1,9 +1,5 @@ package org.broadinstitute.sting.utils.threading; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.util.ArrayList; import java.util.Collection; import java.util.Collections; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java index 3eb2be96b..0f47da413 100644 --- a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java +++ b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java @@ -6,10 +6,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; -import java.io.FileNotFoundException; import java.io.IOException; -import java.io.RandomAccessFile; -import java.nio.channels.*; /** * User: depristo diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java index dec69f7c2..d70879a0a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java +++ b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java @@ -2,13 +2,8 @@ package org.broadinstitute.sting.utils.threading; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.io.RandomAccessFile; -import java.nio.channels.*; /** * User: depristo diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java index 901de6fae..c3f437f11 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.utils.variantcontext; -import java.util.Arrays; -import java.util.List; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collection; +import java.util.List; /** * Immutable representation of an allele diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java index 3feaf5e1c..dba16cf86 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java @@ -24,8 +24,8 @@ package org.broadinstitute.sting.utils.variantcontext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broad.tribble.TribbleException; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; public class GenotypeLikelihoods { public static final boolean CAP_PLS = false; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java index 4efba8825..a191670a4 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java @@ -1,7 +1,10 @@ package org.broadinstitute.sting.utils.variantcontext; -import java.util.*; +import java.util.Collection; +import java.util.Map; +import java.util.Set; +import java.util.TreeMap; /** * Mutable version of VariantContext diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 92c5d648b..eab392c4d 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -2,8 +2,8 @@ package org.broadinstitute.sting.utils.variantcontext; import org.broad.tribble.Feature; import org.broad.tribble.TribbleException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFParser; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index 5d58954aa..5a5671056 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -23,21 +23,26 @@ package org.broadinstitute.sting.utils.variantcontext; -import java.io.Serializable; -import java.util.*; - -import com.google.java.contract.*; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.samtools.util.StringUtil; -import org.apache.commons.jexl2.*; +import org.apache.commons.jexl2.Expression; +import org.apache.commons.jexl2.JexlEngine; import org.broad.tribble.util.popgen.HardyWeinbergCalculation; -import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec; import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker; -import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import java.io.Serializable; +import java.util.*; + public class VariantContextUtils { final public static JexlEngine engine = new JexlEngine(); static { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java index c5a3b6f2a..a59ed7abe 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java @@ -29,7 +29,10 @@ import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.UserException; -import java.util.*; +import java.util.Collection; +import java.util.HashMap; +import java.util.Map; +import java.util.Set; /** * diff --git a/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java b/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java index ab91d0e2e..5782c2704 100755 --- a/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils.wiggle; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.*; From 0a0363aef23e25f876034928eae7e4b3fff08623 Mon Sep 17 00:00:00 2001 From: Matt Hanna Date: Sun, 17 Jul 2011 20:43:35 -0400 Subject: [PATCH 33/39] Revving Picard to get a parser that works with the latest metrics file formats we're starting to see. --- ...1941.jar => picard-private-parts-1954.jar} | Bin 36047 -> 36047 bytes .../picard-private-parts-1954.xml | 3 +++ ...941.xml => picard-private-parts-1954.xml~} | 0 ...icard-1.47.869.jar => picard-1.48.889.jar} | Bin 1084255 -> 1106870 bytes .../repository/net.sf/picard-1.48.889.xml | 3 +++ ...card-1.47.869.xml => picard-1.48.889.xml~} | 0 settings/repository/net.sf/sam-1.47.869.xml | 3 --- .../{sam-1.47.869.jar => sam-1.48.889.jar} | Bin 535562 -> 536180 bytes settings/repository/net.sf/sam-1.48.889.xml | 3 +++ 9 files changed, 9 insertions(+), 3 deletions(-) rename settings/repository/edu.mit.broad/{picard-private-parts-1941.jar => picard-private-parts-1954.jar} (88%) create mode 100644 settings/repository/edu.mit.broad/picard-private-parts-1954.xml rename settings/repository/edu.mit.broad/{picard-private-parts-1941.xml => picard-private-parts-1954.xml~} (100%) rename settings/repository/net.sf/{picard-1.47.869.jar => picard-1.48.889.jar} (87%) create mode 100644 settings/repository/net.sf/picard-1.48.889.xml rename settings/repository/net.sf/{picard-1.47.869.xml => picard-1.48.889.xml~} (100%) delete mode 100644 settings/repository/net.sf/sam-1.47.869.xml rename settings/repository/net.sf/{sam-1.47.869.jar => sam-1.48.889.jar} (91%) create mode 100644 settings/repository/net.sf/sam-1.48.889.xml diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1941.jar b/settings/repository/edu.mit.broad/picard-private-parts-1954.jar similarity index 88% rename from settings/repository/edu.mit.broad/picard-private-parts-1941.jar rename to settings/repository/edu.mit.broad/picard-private-parts-1954.jar index 760db5cb8e7fbcd12b9cd90049ff2ff9ba037b11..67637d3d9311d10767c5758006471a628c5a8a88 100644 GIT binary patch delta 633 zcmX>qR2NBc{P{|ft1A@W_2KST^>yRR0dI#r^ zWqet|GSW&tEMSpUYVX*=jM;jtI6;iblAQXJ_gnBFxfJAz2^Jn;Ww$NuzXyj1DIae=mm1j_aoAl(vO;#ZG zq~;v3lKkc*Fny&t6Rgys#Sg4>Vhcq4TT3FCAJrNIrgyd`foZw6P_X*4wg@o)Vp|oM z_G?cA)7#tQ!L(!tM1O5ZI@q4)9mQbr*v>?-{)3&aU~$f_FtB)1R~(o=+y!x;QFjKI SKesy?O#kjq0jp2y$prxRP5Jr& delta 633 zcmX>|n-hy;Ynb#$-uO{mJ_+c#vEQa>WD-53sV^7Jng@+_n;B28(>Q z-NgoGY;e(mNZogR53&DZ&<=>2p0HVrV25Z%n1a8}U*`}6+Hbe8 zf@h^5GXp~b8v}#wWJWus$pzhVn+po0Ax8BT-(Ui3$SjM8Sa-TSpMx0~nv-oCEWnmj zG}wbwOy1R?52oKV7=vl0MoX}KT%!Y+UfAdb7Jt{64d%x*d4l70E2e^Pyhe` diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1954.xml b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml new file mode 100644 index 000000000..c702fd6e5 --- /dev/null +++ b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1941.xml b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml~ similarity index 100% rename from settings/repository/edu.mit.broad/picard-private-parts-1941.xml rename to settings/repository/edu.mit.broad/picard-private-parts-1954.xml~ diff --git a/settings/repository/net.sf/picard-1.47.869.jar b/settings/repository/net.sf/picard-1.48.889.jar similarity index 87% rename from settings/repository/net.sf/picard-1.47.869.jar rename to settings/repository/net.sf/picard-1.48.889.jar index 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+ +import org.broadinstitute.sting.WalkerTest; +import org.testng.annotations.Test; + +import java.util.Arrays; + +public class PhaseByTransmissionIntegrationTest extends WalkerTest { + private static String phaseByTransmissionTestDataRoot = validationDataLocation + "/PhaseByTransmission"; + private static String fundamentalTestVCF = phaseByTransmissionTestDataRoot + "/" + "FundamentalsTest.unfiltered.vcf"; + + @Test + public void testBasicFunctionalityWithoutFilters() { + WalkerTestSpec spec = new WalkerTestSpec( + buildCommandLine( + "-T PhaseByTransmission", + "-R " + b37KGReference, + "-B:variant,VCF " + fundamentalTestVCF, + "-f NA12892+NA12891=NA12878", + "-nofilters", + "-o %s" + ), + 1, + Arrays.asList("") + ); + executeTest("testBasicFunctionalityWithoutFilters", spec); + } + + @Test + public void testBasicFunctionalityWithFilters() { + WalkerTestSpec spec = new WalkerTestSpec( + buildCommandLine( + "-T PhaseByTransmission", + "-R " + b37KGReference, + "-B:variant,VCF " + fundamentalTestVCF, + "-f NA12892+NA12891=NA12878", + "-o %s" + ), + 1, + Arrays.asList("") + ); + executeTest("testBasicFunctionalityWithFilters", spec); + } +} From afb506e12833b9a82809d58baa02ab30eafd0177 Mon Sep 17 00:00:00 2001 From: Kiran V Garimella Date: Sun, 17 Jul 2011 21:55:33 -0400 Subject: [PATCH 36/39] Added MD5s for PhaseByTransmission integration tests --- .../walkers/phasing/PhaseByTransmissionIntegrationTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java index c8b54e36e..9f59adeb6 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java @@ -21,7 +21,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("") + Arrays.asList("416a483e87358cdcb0b09a496e3254c0") ); executeTest("testBasicFunctionalityWithoutFilters", spec); } @@ -37,7 +37,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("") + Arrays.asList("8c5db343567e90e97993912c7e541d0d") ); executeTest("testBasicFunctionalityWithFilters", spec); } From 8167aba601c5d660e17b2407f090e3d9c61884e0 Mon Sep 17 00:00:00 2001 From: Kiran V Garimella Date: Sun, 17 Jul 2011 22:47:32 -0400 Subject: [PATCH 37/39] Moved (poorly named) MergeAndMatchHaplotypes to public. Added integration test --- .../phasing/MergeAndMatchHaplotypes.java | 107 ++++++++++++++++++ ...ergeAndMatchHaplotypesIntegrationTest.java | 28 +++++ 2 files changed, 135 insertions(+) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java create mode 100644 public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java new file mode 100644 index 000000000..4da049b39 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java @@ -0,0 +1,107 @@ +package org.broadinstitute.sting.gatk.walkers.phasing; + +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; + +import java.util.*; + +public class MergeAndMatchHaplotypes extends RodWalker { + @Output + protected VCFWriter vcfWriter = null; + + private Map pbtCache = new HashMap(); + private Map rbpCache = new HashMap(); + + private final String SOURCE_NAME = "MergeReadBackedAndTransmissionPhasedVariants"; + + public void initialize() { + ArrayList rodNames = new ArrayList(); + rodNames.add("pbt"); + + Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); + Set vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); + Set headerLines = new HashSet(); + headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit())); + + vcfWriter.writeHeader(new VCFHeader(headerLines, vcfSamples)); + } + + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (tracker != null) { + Collection pbts = tracker.getVariantContexts(ref, "pbt", null, ref.getLocus(), true, true); + Collection rbps = tracker.getVariantContexts(ref, "rbp", null, ref.getLocus(), true, true); + + VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null; + VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null; + + if (pbt != null && rbp != null) { + Map genotypes = pbt.getGenotypes(); + + if (!rbp.isFiltered()) { + for (String sample : rbp.getSampleNames()) { + Genotype rbpg = rbp.getGenotype(sample); + Genotype pbtg = pbt.getGenotype(sample); + + // Propagate read-backed phasing information to genotypes unphased by transmission + //if (!pbtg.isPhased() && rbpCache.containsKey(sample)) { + if (!pbtg.isPhased() && rbpg.isPhased() && rbpCache.containsKey(sample)) { + boolean orientationMatches = rbpCache.get(sample).sameGenotype(pbtCache.get(sample), false); + + if (orientationMatches) { + pbtg = rbpg; + } else { + List fwdAlleles = rbpg.getAlleles(); + List revAlleles = new ArrayList(); + + for (int i = fwdAlleles.size() - 1; i >= 0; i--) { + revAlleles.add(fwdAlleles.get(i)); + } + + pbtg = new Genotype(sample, revAlleles, rbpg.getNegLog10PError(), rbpg.getFilters(), rbpg.getAttributes(), rbpg.isPhased()); + } + } + + genotypes.put(sample, pbtg); + + // Update the cache + if (/*rbpg.isPhased() &&*/ rbpg.isHet()) { + rbpCache.put(sample, rbpg); + pbtCache.put(sample, pbtg); + } else if (!rbpg.isPhased()) { + rbpCache.remove(sample); + pbtCache.remove(sample); + } + } + } + + VariantContext newvc = new VariantContext(SOURCE_NAME, pbt.getChr(), pbt.getStart(), pbt.getStart(), pbt.getAlleles(), genotypes, pbt.getNegLog10PError(), pbt.getFilters(), pbt.getAttributes()); + vcfWriter.add(newvc, ref.getBase()); + } + } + + return null; + } + + @Override + public Integer reduceInit() { + return null; + } + + @Override + public Integer reduce(Integer value, Integer sum) { + return null; + } +} diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java new file mode 100644 index 000000000..46d96da27 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java @@ -0,0 +1,28 @@ +package org.broadinstitute.sting.gatk.walkers.phasing; + +import org.broadinstitute.sting.WalkerTest; +import org.testng.annotations.Test; + +import java.util.Arrays; + +public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest { + private static String mergeAndMatchHaplotypesTestDataRoot = validationDataLocation + "/MergeByHaplotypes"; + private static String fundamentalTestPBTVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.vcf"; + private static String fundamentalTestRBPVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.rbp.vcf"; + + @Test + public void testBasicFunctionality() { + WalkerTestSpec spec = new WalkerTestSpec( + buildCommandLine( + "-T MergeAndMatchHaplotypes", + "-R " + b37KGReference, + "-B:pbt,VCF " + fundamentalTestPBTVCF, + "-B:rbp,VCF " + fundamentalTestRBPVCF, + "-o %s" + ), + 1, + Arrays.asList("") + ); + executeTest("testBasicMergeAndMatchHaplotypesFunctionality", spec); + } +} From 824100e57f71d1e98f1fe7940f64cd1837e0a53b Mon Sep 17 00:00:00 2001 From: Kiran V Garimella Date: Sun, 17 Jul 2011 22:50:54 -0400 Subject: [PATCH 38/39] Corrected typo in MergeAndMatchHaplotypes integration test --- .../walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java index 46d96da27..21435dd7d 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java @@ -6,7 +6,7 @@ import org.testng.annotations.Test; import java.util.Arrays; public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest { - private static String mergeAndMatchHaplotypesTestDataRoot = validationDataLocation + "/MergeByHaplotypes"; + private static String mergeAndMatchHaplotypesTestDataRoot = validationDataLocation + "/MergeAndMatchHaplotypes"; private static String fundamentalTestPBTVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.vcf"; private static String fundamentalTestRBPVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.rbp.vcf"; From 497721a799afb09d1ba3042420de4a91f3179daf Mon Sep 17 00:00:00 2001 From: Kiran V Garimella Date: Mon, 18 Jul 2011 00:25:21 -0400 Subject: [PATCH 39/39] Added class documentation string. --- .../sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java index 4da049b39..298d8d6c8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java @@ -17,6 +17,9 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; +/** + * Merges read-back-phased and phase-by-transmission files. + */ public class MergeAndMatchHaplotypes extends RodWalker { @Output protected VCFWriter vcfWriter = null;