zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
View File

@ -357,11 +357,11 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
int offset = p.getOffset();
if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) {
if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) {
continue;
}
if( !gatkRead.containsTemporaryAttribute( SEEN_ATTRIBUTE ) )
if( !gatkRead.containsTemporaryAttribute( SEEN_ATTRIBUTE ) )
{
gatkRead.setTemporaryAttribute( SEEN_ATTRIBUTE, true );
RecalDataManager.parseSAMRecord( gatkRead, RAC );
@ -377,7 +377,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
RecalDataManager.computeCovariates( gatkRead, requestedCovariates ));
}
// Skip this position if base quality is zero
if( gatkRead.getBaseQualities()[offset] > 0 ) {