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Bug fix to previous UnifiedGenotyperEngine refactoring, removed debug code

This commit is contained in:
Guillermo del Angel 2012-03-25 10:20:21 -04:00
parent db54c2625f
commit ce617b2dfc
2 changed files with 3 additions and 3 deletions
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4
build.xml
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@ -955,8 +955,8 @@
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
<jvmarg line="${cofoja.jvm.args}"/>
<jvmarg value="-Xdebug"/>
<jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5678"/>
<!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5678"/> -->
<classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
<classfileset dir="${java.private.test.classes}" erroronmissingdir="false">

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -221,7 +221,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tAFposterior\tNormalizedPosterior");
annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, samples.size());
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, 2*samples.size());
// initialize the header
Set<VCFHeaderLine> headerInfo = getHeaderInfo();