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Merge pull request #790 from broadinstitute/rp_nsubtil_fix-snp-detection 

BQSR bug fix from @nsubtil
This commit is contained in:
rpoplin 2014-12-18 09:19:53 -05:00
parent 071389b507 d84970ff75
commit 4a2ac38308
1 changed files with 6 additions and 0 deletions
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6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java
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@ -313,6 +313,12 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
final boolean[] knownSites = new boolean[readLength];
Arrays.fill(knownSites, false);
for( final Feature f : features ) {
if ((f.getStart() < read.getSoftStart() && f.getEnd() < read.getSoftStart()) ||
(f.getStart() > read.getSoftEnd() && f.getEnd() > read.getSoftEnd())) {
// feature is outside clipping window for the read, ignore
continue;
}
int featureStartOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getStart(), ReadUtils.ClippingTail.LEFT_TAIL, true); // BUGBUG: should I use LEFT_TAIL here?
if( featureStartOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) {
featureStartOnRead = 0;