org.broadinstitute.hellbender.utils.read

Class PrimaryAlignmentKey

java.lang.Object

org.broadinstitute.hellbender.utils.read.PrimaryAlignmentKey

All Implemented Interfaces:

java.lang.Comparable<PrimaryAlignmentKey>

public final class PrimaryAlignmentKey
extends java.lang.Object
implements java.lang.Comparable<PrimaryAlignmentKey>

It is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid). The read name + pairing status should be sufficient for this.

Constructor Summary

Constructors

Constructor and Description
PrimaryAlignmentKey(htsjdk.samtools.SAMRecord rec)

Method Summary

Modifier and Type	Method and Description
int	compareTo(PrimaryAlignmentKey that)
boolean	equals(java.lang.Object o)
int	hashCode()

Methods inherited from class java.lang.Object

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

Constructor Detail

PrimaryAlignmentKey

public PrimaryAlignmentKey(htsjdk.samtools.SAMRecord rec)

Method Detail

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

compareTo

public int compareTo(PrimaryAlignmentKey that)

Specified by:

compareTo in interface java.lang.Comparable<PrimaryAlignmentKey>