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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-11-20 23:20:33 -05:00
parent c2efb04657 c54fc94505
commit 2e1a055aca
1 changed files with 13 additions and 4 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -268,16 +268,25 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
}
protected boolean[] calculateKnownSites( final GATKSAMRecord read, final List<Feature> features ) {
final int BUFFER_SIZE = 0;
final int readLength = read.getReadBases().length;
final boolean[] knownSites = new boolean[readLength];
Arrays.fill(knownSites, false);
for( final Feature f : features ) {
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; }
if( featureStartOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) {
featureStartOnRead = 0;
}
int featureEndOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getEnd(), ReadUtils.ClippingTail.LEFT_TAIL, true);
if( featureEndOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { featureEndOnRead = readLength; }
Arrays.fill(knownSites, Math.max(0, featureStartOnRead - BUFFER_SIZE), Math.min(readLength, featureEndOnRead + 1 + BUFFER_SIZE), true);
if( featureEndOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) {
featureEndOnRead = readLength;
}
if( featureStartOnRead > readLength ) {
featureStartOnRead = featureEndOnRead = readLength;
}
Arrays.fill(knownSites, Math.max(0, featureStartOnRead), Math.min(readLength, featureEndOnRead + 1), true);
}
return knownSites;
}