break;
case S:
// soft clipping - just skip this bit of the read
+ seq.addSequenceFeature(new SequenceFeature("SOFTCLIP", "",
+ nextPos + 1, nextPos + length, "bamfile"));
+ break;
case H:
// hard clipping - this stretch will not appear in the read
+ seq.addSequenceFeature(new SequenceFeature("HARDCLIP", "",
+ nextPos + 1, nextPos + length, "bamfile"));
+ break;
default:
break;
}