Class SAMRecordQueryNameComparator

    • Constructor Detail

      • SAMRecordQueryNameComparator

        public SAMRecordQueryNameComparator()
    • Method Detail

      • fileOrderCompare

        public int fileOrderCompare​(SAMRecord samRecord1,
                                    SAMRecord samRecord2)
        Less stringent compare method than the regular compare. If the two records are equal enough that their ordering in a sorted SAM file would be arbitrary, this method returns 0.
        Specified by:
        fileOrderCompare in interface SAMRecordComparator
        Returns:
        negative if samRecord1 < samRecord2, 0 if equal, else positive
      • compareReadNames

        public static int compareReadNames​(String readName1,
                                           String readName2)
        Encapsulate algorithm for comparing read names in queryname-sorted file, since there have been conversations about changing the behavior.