Package de.charite.compbio.jannovar.mendel.filter

Class CoordinateSortingChecker

java.lang.Object

de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker

All Implemented Interfaces:

VariantContextProcessor, Closeable, AutoCloseable

public class CoordinateSortingChecker
extends Object
implements VariantContextProcessor

Check that the VCF file is sorted by coordinate

Since VCF files do not have to provide a reference name dictionary in their header, validating the sort order of the chromosomes is tricky. Instead, we check that there is no run of VCF records for a chromosome, something on a different chromsome, and then a previous one again. Within one chromosome, we check by change begin position.

In case of problems, put(htsjdk.variant.variantcontext.VariantContext) throws a VariantContextFilterException.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
CoordinateSortingChecker(VariantContextProcessor sink)	Initialize the checker

Method Summary

Modifier and Type	Method	Description
void	close()	Mark processing as done, no more variants will come in.
void	put(htsjdk.variant.variantcontext.VariantContext vc)	Put a Variant Context into the filter.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CoordinateSortingChecker

public CoordinateSortingChecker(VariantContextProcessor sink)

Initialize the checker

Method Detail

put

public void put(htsjdk.variant.variantcontext.VariantContext vc)
         throws VariantContextFilterException

Description copied from interface: VariantContextProcessor

Put a Variant Context into the filter.

Specified by:

put in interface VariantContextProcessor

Parameters:

vc - VariantContext to put into the filter.

Throws:

VariantContextFilterException - on problems during the filtration

close

public void close()

Description copied from interface: VariantContextProcessor

Mark processing as done, no more variants will come in.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface VariantContextProcessor