/**
* Determines what is the position of the read in relation to the interval. Note: This function
* uses the UNCLIPPED ENDS of the reads for the comparison.
*
* @param read the read
* @param interval the interval
* @return the overlap type as described by ReadAndIntervalOverlap enum (see above)
*/
public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(
GATKSAMRecord read, GenomeLoc interval) {
int sStart = read.getSoftStart();
int sStop = read.getSoftEnd();
int uStart = read.getUnclippedStart();
int uStop = read.getUnclippedEnd();
if (!read.getReferenceName().equals(interval.getContig()))
return ReadAndIntervalOverlap.NO_OVERLAP_CONTIG;
else if (uStop < interval.getStart()) return ReadAndIntervalOverlap.NO_OVERLAP_LEFT;
else if (uStart > interval.getStop()) return ReadAndIntervalOverlap.NO_OVERLAP_RIGHT;
else if (sStop < interval.getStart()) return ReadAndIntervalOverlap.NO_OVERLAP_HARDCLIPPED_LEFT;
else if (sStart > interval.getStop())
return ReadAndIntervalOverlap.NO_OVERLAP_HARDCLIPPED_RIGHT;
else if ((sStart >= interval.getStart()) && (sStop <= interval.getStop()))
return ReadAndIntervalOverlap.OVERLAP_CONTAINED;
else if ((sStart < interval.getStart()) && (sStop > interval.getStop()))
return ReadAndIntervalOverlap.OVERLAP_LEFT_AND_RIGHT;
else if ((sStart < interval.getStart())) return ReadAndIntervalOverlap.OVERLAP_LEFT;
else return ReadAndIntervalOverlap.OVERLAP_RIGHT;
}
