htsjdk.samtools

Class SAMRecordQueryNameComparator

java.lang.Object

htsjdk.samtools.SAMRecordQueryNameComparator

All Implemented Interfaces:

SAMRecordComparator, java.util.Comparator<SAMRecord>

public class SAMRecordQueryNameComparator
extends java.lang.Object
implements SAMRecordComparator

Comparator for "queryname" ordering of SAMRecords.

Constructor Summary

Constructors

Constructor and Description
SAMRecordQueryNameComparator()

Method Summary

Methods

Modifier and Type	Method and Description
int	compare(SAMRecord samRecord1, SAMRecord samRecord2)
static int	compareReadNames(java.lang.String readName1, java.lang.String readName2) Encapsulate algorithm for comparing read names in queryname-sorted file, since there have been conversations about changing the behavior.
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

equals

Constructor Detail

SAMRecordQueryNameComparator

public SAMRecordQueryNameComparator()

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.

Specified by:

fileOrderCompare in interface SAMRecordComparator

Returns:

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

compareReadNames

public static int compareReadNames(java.lang.String readName1,
                   java.lang.String readName2)

Encapsulate algorithm for comparing read names in queryname-sorted file, since there have been conversations about changing the behavior.