Package htsjdk.samtools

Class SAMRecordQueryHashComparator

java.lang.Object

htsjdk.samtools.SAMRecordQueryNameComparator

htsjdk.samtools.SAMRecordQueryHashComparator

All Implemented Interfaces:

SAMRecordComparator, Serializable, Comparator<SAMRecord>

public class SAMRecordQueryHashComparator
extends SAMRecordQueryNameComparator
implements Serializable

SAMRecord comparator that provides an ordering based on a hash of the queryname. Has the useful property that reads with the same name will be grouped together, but that reads appear in an otherwise random order. Useful for when the read names in a BAM are correlated to something else (e.g. position, read group), making a straight queryname sort undesirable.

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
SAMRecordQueryHashComparator()

Method Summary

Modifier and Type	Method	Description
int	compare(SAMRecord lhs, SAMRecord rhs)	Compares two records based on an integer hash of their read name's.
int	fileOrderCompare(SAMRecord lhs, SAMRecord rhs)	Compares two records based on an integer hash of their read names.

Methods inherited from class htsjdk.samtools.SAMRecordQueryNameComparator

compareReadNames

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, reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Constructor Details

SAMRecordQueryHashComparator

public SAMRecordQueryHashComparator()

Method Details

compare

public int compare(SAMRecord lhs,
 SAMRecord rhs)

Compares two records based on an integer hash of their read name's. If the hash values are equal, falls back to the behaviour of SAMRecordQueryNameComparator to break the tie.

Specified by:

compare in interface Comparator<SAMRecord>

Overrides:

compare in class SAMRecordQueryNameComparator

fileOrderCompare

public int fileOrderCompare(SAMRecord lhs,
 SAMRecord rhs)

Compares two records based on an integer hash of their read names. If the hash values are equal, falls back to the behaviour of SAMRecordQueryNameComparator to break the tie.

Specified by:

fileOrderCompare in interface SAMRecordComparator

Overrides:

fileOrderCompare in class SAMRecordQueryNameComparator

Returns:

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