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

When adding a unit test to LIBS for X and = CIGAR operators, I uncovered a bug with the implementation of the ReadBackedPileup.depthOfCoverage() method.

This commit is contained in:
Eric Banks 2012-08-10 14:58:29 -04:00
parent eca9613356
commit 40f0320a1c
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -155,7 +155,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
protected void addPileupToCumulativeStats(AbstractReadBackedPileup<RBP, PE> pileup) { protected void addPileupToCumulativeStats(AbstractReadBackedPileup<RBP, PE> pileup) {
size += pileup.getNumberOfElements(); size += pileup.getNumberOfElements();
abstractSize += pileup.depthOfCoverage(); abstractSize = pileup.depthOfCoverage() + (abstractSize == -1 ? 0 : abstractSize);
nDeletions += pileup.getNumberOfDeletions(); nDeletions += pileup.getNumberOfDeletions();
nMQ0Reads += pileup.getNumberOfMappingQualityZeroReads(); nMQ0Reads += pileup.getNumberOfMappingQualityZeroReads();
} }