/**
* Try to fix the given read using the given split
*
* @param read the read to fix
* @param splice the split (bad region to clip out)
*/
private void fixSplit(final SplitRead read, final Splice splice) {
// if the read doesn't even overlap the split position then we can just exit
if (read.loc == null || !splice.loc.overlapsP(read.loc)) return;
if (isLeftOverhang(read.loc, splice.loc)) {
final int overhang = splice.loc.getStop() - read.loc.getStart() + 1;
if (overhangingBasesMismatch(
read.read.getBases(),
0,
splice.reference,
splice.reference.length - overhang,
overhang)) {
final GATKRead clippedRead =
ReadClipper.hardClipByReadCoordinates(read.read, 0, overhang - 1);
read.setRead(clippedRead);
}
} else if (isRightOverhang(read.loc, splice.loc)) {
final int overhang = read.loc.getStop() - splice.loc.getStart() + 1;
if (overhangingBasesMismatch(
read.read.getBases(), read.read.getLength() - overhang, splice.reference, 0, overhang)) {
final GATKRead clippedRead =
ReadClipper.hardClipByReadCoordinates(
read.read, read.read.getLength() - overhang, read.read.getLength() - 1);
read.setRead(clippedRead);
}
}
}
/**
* Given a read, clips low quality ends (by overwriting with N) and returns the underlying bases,
* after reverse-complementing for negative-strand reads.
*
* @param read the read
* @param lowQTail every base quality lower than or equal to this in the tail of the read will be
* replaced with N.
* @return bases of the read.
*/
public static byte[] getStrandedBytes(final SAMRecord read, final byte lowQTail) {
// Write N's over the low quality tail of the reads to avoid adding them into the context
final SAMRecord clippedRead =
ReadClipper.clipLowQualEnds(read, lowQTail, ClippingRepresentation.WRITE_NS);
final byte[] bases = clippedRead.getReadBases();
if (read.getReadNegativeStrandFlag()) {
return BaseUtils.simpleReverseComplement(bases);
} else {
return bases;
}
}