/**
* Hard clip bases from read, from start to stop in base coordinates
*
* <p>If start == 0, then we will clip from the front of the read, otherwise we clip from the
* right. If start == 0 and stop == 10, this would clip out the first 10 bases of the read.
*
* <p>Note that this function works with reads with negative alignment starts, in order to allow
* us to hardClip reads that have had their soft clips reverted and so might have negative
* alignment starts
*
* <p>Works properly with reduced reads and insertion/deletion base qualities
*
* @param read a non-null read
* @param start a start >= 0 and < read.length
* @param stop a stop >= 0 and < read.length.
* @return a cloned version of read that has been properly trimmed down
*/
private GATKSAMRecord hardClip(GATKSAMRecord read, int start, int stop) {
// If the read is unmapped there is no Cigar string and neither should we create a new cigar
// string
final CigarShift cigarShift =
(read.getReadUnmappedFlag())
? new CigarShift(new Cigar(), 0, 0)
: hardClipCigar(read.getCigar(), start, stop);
// the cigar may force a shift left or right (or both) in case we are left with insertions
// starting or ending the read after applying the hard clip on start/stop.
final int newLength =
read.getReadLength()
- (stop - start + 1)
- cigarShift.shiftFromStart
- cigarShift.shiftFromEnd;
final byte[] newBases = new byte[newLength];
final byte[] newQuals = new byte[newLength];
final int copyStart =
(start == 0) ? stop + 1 + cigarShift.shiftFromStart : cigarShift.shiftFromStart;
System.arraycopy(read.getReadBases(), copyStart, newBases, 0, newLength);
System.arraycopy(read.getBaseQualities(), copyStart, newQuals, 0, newLength);
final GATKSAMRecord hardClippedRead = (GATKSAMRecord) read.clone();
hardClippedRead
.resetSoftStartAndEnd(); // reset the cached soft start and end because they may have
// changed now that the read was hard clipped. No need to calculate
// them now. They'll be lazily calculated on the next call to
// getSoftStart()/End()
hardClippedRead.setBaseQualities(newQuals);
hardClippedRead.setReadBases(newBases);
hardClippedRead.setCigar(cigarShift.cigar);
if (start == 0)
hardClippedRead.setAlignmentStart(
read.getAlignmentStart()
+ calculateAlignmentStartShift(read.getCigar(), cigarShift.cigar));
if (read.hasBaseIndelQualities()) {
final byte[] newBaseInsertionQuals = new byte[newLength];
final byte[] newBaseDeletionQuals = new byte[newLength];
System.arraycopy(
read.getBaseInsertionQualities(), copyStart, newBaseInsertionQuals, 0, newLength);
System.arraycopy(
read.getBaseDeletionQualities(), copyStart, newBaseDeletionQuals, 0, newLength);
hardClippedRead.setBaseQualities(newBaseInsertionQuals, EventType.BASE_INSERTION);
hardClippedRead.setBaseQualities(newBaseDeletionQuals, EventType.BASE_DELETION);
}
return hardClippedRead;
}
