public BAQCalculationResult calcBAQFromHMM(SAMRecord read, IndexedFastaSequenceFile refReader) {
// start is alignment start - band width / 2 - size of first I element, if there is one. Stop
// is similar
int offset = getBandWidth() / 2;
long readStart = includeClippedBases ? read.getUnclippedStart() : read.getAlignmentStart();
long start = Math.max(readStart - offset - ReadUtils.getFirstInsertionOffset(read), 0);
long stop =
(includeClippedBases ? read.getUnclippedEnd() : read.getAlignmentEnd())
+ offset
+ ReadUtils.getLastInsertionOffset(read);
if (stop
> refReader
.getSequenceDictionary()
.getSequence(read.getReferenceName())
.getSequenceLength()) {
return null;
} else {
// now that we have the start and stop, get the reference sequence covering it
ReferenceSequence refSeq = refReader.getSubsequenceAt(read.getReferenceName(), start, stop);
return calcBAQFromHMM(read, refSeq.getBases(), (int) (start - readStart));
}
}
