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The allele biased downsampling should not abort if there's a reduced read. Rather it should always keep the RR and downsample only original reads in the pileup.

This commit is contained in:
Eric Banks 2012-12-05 23:15:36 -05:00
parent dbf721968d
commit 406adb8d44
1 changed files with 6 additions and 2 deletions
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8
protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
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@ -56,11 +56,14 @@ public class AlleleBiasedDownsamplingUtils {
for ( int i = 0; i < 4; i++ ) for ( int i = 0; i < 4; i++ )
alleleStratifiedElements[i] = new ArrayList<PileupElement>(); alleleStratifiedElements[i] = new ArrayList<PileupElement>();
// keep all of the reduced reads
final ArrayList<PileupElement> reducedReadPileups = new ArrayList<PileupElement>();
// start by stratifying the reads by the alleles they represent at this position // start by stratifying the reads by the alleles they represent at this position
for( final PileupElement pe : pileup ) { for( final PileupElement pe : pileup ) {
// abort if we have a reduced read - we do not want to remove it! // we do not want to remove a reduced read
if ( pe.getRead().isReducedRead() ) if ( pe.getRead().isReducedRead() )
return pileup; reducedReadPileups.add(pe);
final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase()); final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase());
if ( baseIndex != -1 ) if ( baseIndex != -1 )
@ -76,6 +79,7 @@ public class AlleleBiasedDownsamplingUtils {
return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName()); return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName());
} }
}); });
elementsToKeep.addAll(reducedReadPileups);
// make a listing of allele counts // make a listing of allele counts
final int[] alleleCounts = new int[4]; final int[] alleleCounts = new int[4];