/**
* Generic functionality to hard clip a read, used internally by
* hardClipByReferenceCoordinatesLeftTail and hardClipByReferenceCoordinatesRightTail. Should not
* be used directly.
*
* <p>Note, it REQUIRES you to give the directionality of your hard clip (i.e. whether you're
* clipping the left of right tail) by specifying either refStart < 0 or refStop < 0.
*
* @param refStart first base to clip (inclusive)
* @param refStop last base to clip (inclusive)
* @return a new read, without the clipped bases
*/
@Requires({
"!read.getReadUnmappedFlag()",
"refStart < 0 || refStop < 0"
}) // can't handle unmapped reads, as we're using reference coordinates to clip
protected GATKSAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
if (read.isEmpty()) return read;
int start;
int stop;
// Determine the read coordinate to start and stop hard clipping
if (refStart < 0) {
if (refStop < 0)
throw new ReviewedStingException(
"Only one of refStart or refStop must be < 0, not both ("
+ refStart
+ ", "
+ refStop
+ ")");
start = 0;
stop =
ReadUtils.getReadCoordinateForReferenceCoordinate(
read, refStop, ReadUtils.ClippingTail.LEFT_TAIL);
} else {
if (refStop >= 0)
throw new ReviewedStingException(
"Either refStart or refStop must be < 0 (" + refStart + ", " + refStop + ")");
start =
ReadUtils.getReadCoordinateForReferenceCoordinate(
read, refStart, ReadUtils.ClippingTail.RIGHT_TAIL);
stop = read.getReadLength() - 1;
}
if (start < 0 || stop > read.getReadLength() - 1)
throw new ReviewedStingException(
"Trying to clip before the start or after the end of a read");
if (start > stop)
throw new ReviewedStingException(
String.format(
"START (%d) > (%d) STOP -- this should never happen, please check read: %s (CIGAR: %s)",
start, stop, read, read.getCigarString()));
if (start > 0 && stop < read.getReadLength() - 1)
throw new ReviewedStingException(
String.format(
"Trying to clip the middle of the read: start %d, stop %d, cigar: %s",
start, stop, read.getCigarString()));
this.addOp(new ClippingOp(start, stop));
GATKSAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);
this.ops = null;
return clippedRead;
}
