Package htsjdk.samtools

Interface SAMRecordComparator

All Superinterfaces:

Comparator<SAMRecord>

All Known Implementing Classes:

SAMRecordCoordinateComparator, SAMRecordDuplicateComparator, SAMRecordQueryHashComparator, SAMRecordQueryNameComparator

public interface SAMRecordComparator
extends Comparator<SAMRecord>

Interface for comparators that define the various SAM sort orders.

Method Summary

Modifier and Type	Method	Description
int	fileOrderCompare(SAMRecord samRecord1, SAMRecord samRecord2)	Less stringent compare method than the regular compare.

Methods inherited from interface java.util.Comparator

compare, equals, reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Method Details

fileOrderCompare

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.

Returns:

negative if samRecord1 < samRecord2, 0 if equal, else positive