htsjdk.samtools

Class SAMRecordCoordinateComparator

java.lang.Object

htsjdk.samtools.SAMRecordCoordinateComparator

All Implemented Interfaces:

SAMRecordComparator, java.io.Serializable, java.util.Comparator<SAMRecord>

public class SAMRecordCoordinateComparator
extends java.lang.Object
implements SAMRecordComparator, java.io.Serializable

Comparator for sorting SAMRecords by coordinate. Note that the header is required because the order of sequences in the header defines the major sort order. Ideally this method would only return 0 for completely equal SAMRecords, so that sort is completely deterministic. This implementation does not achieve this completely, but it comes pretty close, while avoiding decoding the variable length fields, except for read name, which is decoded if coordinate and strand are equal. Extreme care must be taken to ensure the following: if A == B, then B == A if A < B, then B > A if A < B && B < C, then A < C

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SAMRecordCoordinateComparator()

Method Summary

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.Comparator

comparing, comparing, comparingDouble, comparingInt, comparingLong, equals, naturalOrder, nullsFirst, nullsLast, reversed, reverseOrder, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Constructor Detail

SAMRecordCoordinateComparator

public SAMRecordCoordinateComparator()

Method Detail

compare

public int compare(SAMRecord samRecord1,
                   SAMRecord samRecord2)

Specified by:

compare in interface java.util.Comparator<SAMRecord>

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. If read is paired and unmapped, use the mate mapping to sort. Records being compared must have non-null SAMFileHeaders.

Specified by:

fileOrderCompare in interface SAMRecordComparator

Returns:

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