Package htsjdk.variant.variantcontext

Class VariantContextComparator

java.lang.Object

htsjdk.variant.variantcontext.VariantContextComparator

All Implemented Interfaces:

Serializable, Comparator<VariantContext>

public class VariantContextComparator
extends Object
implements Comparator<VariantContext>, 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	Description
VariantContextComparator(SAMSequenceDictionary dictionary)
VariantContextComparator(Collection<VCFContigHeaderLine> headerLines)	Creates a VariantContextComparator from the given VCF contig header lines.
VariantContextComparator(List<String> contigs)

Method Summary

Modifier and Type	Method	Description
int	compare(VariantContext firstVariantContext, VariantContext secondVariantContext)
static List<String>	getSequenceNameList(SAMSequenceDictionary dictionary)
boolean	isCompatible(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

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

Constructor Details

VariantContextComparator

public VariantContextComparator(List<String> contigs)

VariantContextComparator

public VariantContextComparator(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 Details

getSequenceNameList

public static List<String> getSequenceNameList(SAMSequenceDictionary dictionary)

compare

public int compare(VariantContext firstVariantContext,
 VariantContext secondVariantContext)

Specified by:

compare in interface Comparator<VariantContext>

isCompatible

public boolean isCompatible(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.