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Fixed memory leak in VariantEval 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3845 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-07-21 12:35:46 +00:00
parent cebddb5bd3
commit f7957bc7f2
2 changed files with 13 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -115,9 +115,15 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
@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};

9
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
View File

@ -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";