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

Better implementation of GATKSAMRecord.getSoftStart()

This commit is contained in:
Eric Banks 2012-10-19 12:11:18 -04:00
parent deca564aef
commit f08e5a44da
1 changed files with 4 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -387,14 +387,10 @@ public class GATKSAMRecord extends BAMRecord {
*/ */
public int getSoftStart() { public int getSoftStart() {
if (softStart < 0) { if (softStart < 0) {
int start = this.getUnclippedStart(); softStart = getAlignmentStart();
for (CigarElement cigarElement : this.getCigar().getCigarElements()) { final CigarElement firstCig = getCigar().getCigarElement(0);
if (cigarElement.getOperator() == CigarOperator.HARD_CLIP) if (firstCig.getOperator() == CigarOperator.HARD_CLIP)
start += cigarElement.getLength(); softStart -= firstCig.getLength();
else
break;
}
softStart = start;
} }
return softStart; return softStart;
} }