- All Implemented Interfaces:
- java.io.Serializable, java.util.Comparator<GATKRead>
public final class ReadCoordinateComparator
extends java.lang.Object
implements java.util.Comparator<GATKRead>, java.io.Serializable
Comparator for sorting Reads by coordinate. Note that a header is required in
order to meaningfully compare contigs.
Uses the various other fields in a read to break ties for reads that share
the same location.
Ordering is almost identical to the SAMRecordCoordinateComparator,
modulo a few subtle differences in tie-breaking rules for reads that share the same
position. This comparator will produce an ordering consistent with coordinate ordering
in a bam file, including interleaving unmapped reads assigned the positions of their
mates with the mapped reads.
- See Also:
- Serialized Form