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

Fixing BQSR bug reported on the forum for reads that begin with insertions.

This commit is contained in:
Ryan Poplin 2012-10-10 16:01:37 -04:00
parent b3cc04976f
commit 45717349dc
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/gatk/walkers/bqsr/BaseRecalibrator.java
View File

@ -225,7 +225,7 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
final GATKSAMRecord read = p.getRead(); final GATKSAMRecord read = p.getRead();
final int offset = p.getOffset(); final int offset = p.getOffset();
if (readHasBeenSkipped(read) || isLowQualityBase(p)) // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases) if (readHasBeenSkipped(read) || p.isInsertionAtBeginningOfRead() || isLowQualityBase(p) ) // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
continue; continue;
if (readNotSeen(read)) { if (readNotSeen(read)) {