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Bringing us back to passing integrationtests 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4904 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-12-23 14:36:11 +00:00
parent 8c583ea405
commit 464d0e18e3
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -792,7 +792,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
}
private List<GenotypeAndReadBases> trimWindow(List<GenotypeAndReadBases> listHetGenotypes, String sample, GenomeLoc phaseLocus) {
logger.warn("Trying to phase sample " + sample + " at locus " + phaseLocus + " within a window of " + cacheWindow + " bases yields " + listHetGenotypes.size() + " heterozygous sites to phase:\n" + toStringGRL(listHetGenotypes));
if ( DEBUG) logger.warn("Trying to phase sample " + sample + " at locus " + phaseLocus + " within a window of " + cacheWindow + " bases yields " + listHetGenotypes.size() + " heterozygous sites to phase:\n" + toStringGRL(listHetGenotypes));
int prevSiteIndex = phasingSiteIndex - 1; // index of previous in listHetGenotypes
int numToUse = maxPhaseSites - 2; // since always keep previous and current het sites!
@ -815,7 +815,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
int stopIndex = phasingSiteIndex + useOnRight + 1; // put the index 1 past the desired index to keep
phasingSiteIndex -= startIndex;
listHetGenotypes = listHetGenotypes.subList(startIndex, stopIndex);
logger.warn("NAIVELY REDUCED to " + listHetGenotypes.size() + " sites:\n" + toStringGRL(listHetGenotypes));
if ( DEBUG ) logger.warn("NAIVELY REDUCED to " + listHetGenotypes.size() + " sites:\n" + toStringGRL(listHetGenotypes));
return listHetGenotypes;
}
@ -1006,7 +1006,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
}
private void writeVCF(VariantContext vc) {
if ( vc.isNotFiltered() )
if ( samplesToPhase == null || vc.isNotFiltered() )
//if ( samplesToPhase == null || (vc.isVariant() && vc.isNotFiltered())) // if we are only operating on specific samples, don't write out all sites, just those where the VC is variant
WriteVCF.writeVCF(vc, writer, logger);
}