htsjdk.variant.variantcontext

Class VariantContextComparator

java.lang.Object

htsjdk.variant.variantcontext.VariantContextComparator

All Implemented Interfaces:

java.io.Serializable, java.util.Comparator<VariantContext>

public class VariantContextComparator
extends java.lang.Object
implements java.util.Comparator<VariantContext>, java.io.Serializable

A Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List provided at construction time, then by start position with each contig/chromosome.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
VariantContextComparator(java.util.Collection<VCFContigHeaderLine> headerLines) Creates a VariantContextComparator from the given VCF contig header lines.
VariantContextComparator(java.util.List<java.lang.String> contigs)
VariantContextComparator(SAMSequenceDictionary dictionary)

Method Summary

Modifier and Type	Method and Description
int	compare(VariantContext firstVariantContext, VariantContext secondVariantContext)
static java.util.List<java.lang.String>	getSequenceNameList(SAMSequenceDictionary dictionary)
boolean	isCompatible(java.util.Collection<VCFContigHeaderLine> headerLines) Returns true if the given header lines are from a file sorted according to this VariantContextComparator.

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

VariantContextComparator

public VariantContextComparator(java.util.List<java.lang.String> contigs)

VariantContextComparator

public VariantContextComparator(java.util.Collection<VCFContigHeaderLine> headerLines)

Creates a VariantContextComparator from the given VCF contig header lines. The header lines' index values are used to order the contigs. Throws IllegalArgumentException if there are dupe

VariantContextComparator

public VariantContextComparator(SAMSequenceDictionary dictionary)

Method Detail

getSequenceNameList

public static java.util.List<java.lang.String> getSequenceNameList(SAMSequenceDictionary dictionary)

compare

public int compare(VariantContext firstVariantContext,
                   VariantContext secondVariantContext)

Specified by:

compare in interface java.util.Comparator<VariantContext>

isCompatible

public boolean isCompatible(java.util.Collection<VCFContigHeaderLine> headerLines)

Returns true if the given header lines are from a file sorted according to this VariantContextComparator. For sorting to work properly, the contig in each header line must have the same index.