returning read instead of GATKSAMRecord

Do not create new GATKSAMRecord when read has been fully clipped, because it is essentially the same as returning the currently fully clipped read.
This commit is contained in:
Mauricio Carneiro 2011-11-18 16:49:59 -05:00
parent f48d4cfa79
commit 333e5de812
1 changed files with 1 additions and 1 deletions

View File

@ -121,7 +121,7 @@ public class ReadClipper {
public GATKSAMRecord hardClipSoftClippedBases () {
if (read.isEmpty())
return new GATKSAMRecord(read.getHeader());
return read;
int readIndex = 0;
int cutLeft = -1; // first position to hard clip (inclusive)