@Override
public int compare(Pair<Integer, File> p1, Pair<Integer, File> p2) {
int startPositionP1 = p1.getFirst();
int startPositionP2 = p2.getFirst();
if (startPositionP1 == startPositionP2) return 0;
return startPositionP1 < startPositionP2 ? -1 : 1;
}
// we need to pad ref by at least the bandwidth / 2 on either side
public BAQCalculationResult calcBAQFromHMM(SAMRecord read, byte[] ref, int refOffset) {
// todo -- need to handle the case where the cigar sum of lengths doesn't cover the whole read
Pair<Integer, Integer> queryRange = calculateQueryRange(read);
if (queryRange == null) return null; // read has Ns, or is completely clipped away
int queryStart = queryRange.getFirst();
int queryEnd = queryRange.getSecond();
BAQCalculationResult baqResult =
calcBAQFromHMM(ref, read.getReadBases(), read.getBaseQualities(), queryStart, queryEnd);
// cap quals
int readI = 0, refI = 0;
for (CigarElement elt : read.getCigar().getCigarElements()) {
int l = elt.getLength();
switch (elt.getOperator()) {
case N: // cannot handle these
return null;
case H:
case P: // ignore pads and hard clips
break;
case S:
refI += l; // move the reference too, in addition to I
case I:
// todo -- is it really the case that we want to treat I and S the same?
for (int i = readI; i < readI + l; i++) baqResult.bq[i] = baqResult.rawQuals[i];
readI += l;
break;
case D:
refI += l;
break;
case M:
for (int i = readI; i < readI + l; i++) {
int expectedPos = refI - refOffset + (i - readI);
baqResult.bq[i] =
capBaseByBAQ(
baqResult.rawQuals[i], baqResult.bq[i], baqResult.state[i], expectedPos);
}
readI += l;
refI += l;
break;
default:
throw new ReviewedGATKException(
"BUG: Unexpected CIGAR element " + elt + " in read " + read.getReadName());
}
}
if (readI != read.getReadLength()) // odd cigar string
System.arraycopy(baqResult.rawQuals, 0, baqResult.bq, 0, baqResult.bq.length);
return baqResult;
}
/**
* General interval reduce routine called after all of the traversals are done
*
* @param results interval reduce results
*/
public void onTraversalDone(List<Pair<GenomeLoc, ReduceType>> results) {
for (Pair<GenomeLoc, ReduceType> result : results) {
logger.info(String.format("[INTERVAL REDUCE RESULT] at %s ", result.getFirst()));
this.onTraversalDone(result.getSecond());
}
}