/**
* Hard clips away soft clipped bases that are below the given quality threshold
*
* @param read the read
* @param minQual the mininum base quality score to revert the base (inclusive)
* @return a new read without low quality soft clipped bases
*/
public static GATKSAMRecord hardClipLowQualitySoftClips(GATKSAMRecord read, byte minQual) {
int nLeadingSoftClips = read.getAlignmentStart() - read.getSoftStart();
if (read.isEmpty() || nLeadingSoftClips > read.getReadLength())
return GATKSAMRecord.emptyRead(read);
byte[] quals = read.getBaseQualities(EventType.BASE_SUBSTITUTION);
int left = -1;
if (nLeadingSoftClips > 0) {
for (int i = nLeadingSoftClips - 1; i >= 0; i--) {
if (quals[i] >= minQual) left = i;
else break;
}
}
int right = -1;
int nTailingSoftClips = read.getSoftEnd() - read.getAlignmentEnd();
if (nTailingSoftClips > 0) {
for (int i = read.getReadLength() - nTailingSoftClips; i < read.getReadLength(); i++) {
if (quals[i] >= minQual) right = i;
else break;
}
}
GATKSAMRecord clippedRead = read;
if (right >= 0
&& right + 1
< clippedRead
.getReadLength()) // only clip if there are softclipped bases (right >= 0) and the
// first high quality soft clip is not the last base (right+1 <
// readlength)
clippedRead =
hardClipByReadCoordinates(
clippedRead,
right + 1,
clippedRead.getReadLength()
- 1); // first we hard clip the low quality soft clips on the right tail
if (left >= 0
&& left - 1
> 0) // only clip if there are softclipped bases (left >= 0) and the first high quality
// soft clip is not the last base (left-1 > 0)
clippedRead =
hardClipByReadCoordinates(
clippedRead,
0,
left - 1); // then we hard clip the low quality soft clips on the left tail
return clippedRead;
}
