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Updating HaplotypeCaller's HMM calc to use GOP as a function of the read instead of a function of the haplotype in preparation for IQSR

This commit is contained in:
Ryan Poplin 2012-02-02 10:17:04 -05:00
parent 2109122cdd
commit 4ed06801a7
1 changed files with 2 additions and 3 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
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@ -357,11 +357,11 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead(); final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
int offset = p.getOffset(); int offset = p.getOffset();
if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) { if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) {
continue; continue;
} }
if( !gatkRead.containsTemporaryAttribute( SEEN_ATTRIBUTE ) ) if( !gatkRead.containsTemporaryAttribute( SEEN_ATTRIBUTE ) )
{ {
gatkRead.setTemporaryAttribute( SEEN_ATTRIBUTE, true ); gatkRead.setTemporaryAttribute( SEEN_ATTRIBUTE, true );
RecalDataManager.parseSAMRecord( gatkRead, RAC ); RecalDataManager.parseSAMRecord( gatkRead, RAC );
@ -377,7 +377,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
RecalDataManager.computeCovariates( gatkRead, requestedCovariates )); RecalDataManager.computeCovariates( gatkRead, requestedCovariates ));
} }
// Skip this position if base quality is zero // Skip this position if base quality is zero
if( gatkRead.getBaseQualities()[offset] > 0 ) { if( gatkRead.getBaseQualities()[offset] > 0 ) {