From f7957bc7f24aa05f5fa4160f693ba0fc36754204 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 21 Jul 2010 12:35:46 +0000 Subject: [PATCH] Fixed memory leak in VariantEval git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3845 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/varianteval/VariantEvalWalker.java | 8 +++++++- .../walkers/varianteval/AminoAcidTransition.java | 9 ++++++--- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 436376bfa..c745663c3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -115,9 +115,15 @@ public class VariantEvalWalker extends RodWalker { @Argument(shortName="select", doc="One or more stratifications to use when evaluating the data", required=false) protected String[] SELECT_EXPS = {}; - + //protected String[] SELECT_EXPS = {"set == \"Intersection\"", + // "set == \"HiSeq.WGS.cleaned.ug.vcf\"", + // "set == \"HiSeq.WGS.cleaned.ug.vcf\" || set == \"Intersection\"", + // "set == \"HiSeq.WGS.raw.OQ.ug.vcf\"", + // "set == \"HiSeq.WGS.raw.OQ.ug.vcf\" || set == \"Intersection\""}; + @Argument(shortName="selectName", doc="Names to use for the list of stratifications (must be a 1-to-1 mapping)", required=false) protected String[] SELECT_NAMES = {}; + //protected String[] SELECT_NAMES = {"Intersection", "x1", "x2", "x3", "x4"}; @Argument(shortName="known", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false) protected String[] KNOWN_NAMES = {DbSNPHelper.STANDARD_DBSNP_TRACK_NAME}; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java index 8954ab45b..8bd27d389 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java @@ -133,9 +133,11 @@ public class AminoAcidTransition extends VariantEvaluator { public AminoAcidTransition(VariantEvalWalker parent) { super(parent); enabled = parent.aminoAcidTransitionKey != null; - getParsingInformation(parent); - lookup = new AminoAcidTable(); - acidTable = new AminoAcidTiTvTable(); + if ( enabled ) { + getParsingInformation(parent); + lookup = new AminoAcidTable(); + acidTable = new AminoAcidTiTvTable(); + } } private void getParsingInformation(VariantEvalWalker parent) { @@ -172,6 +174,7 @@ public class AminoAcidTransition extends VariantEvaluator { public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { String interesting = null; if ( eval != null && eval.hasAttribute(infoKey) ) { + //if ( enabled && eval != null && eval.hasAttribute(infoKey) ) { String[] parsedNames = ( (String) eval.getAttribute(infoKey)).split(infoValueSplit); String first = "none"; String second = "none";