picard.vcf.processor

Class VcfFileSegmentGenerator

java.lang.Object

picard.vcf.processor.VcfFileSegmentGenerator

public abstract class VcfFileSegmentGenerator
extends java.lang.Object

Describes a mechanism for producing VcfFileSegments from a VCF file.

Constructor Summary

Constructors

Constructor and Description
VcfFileSegmentGenerator()

Method Summary

Modifier and Type	Method and Description
static VcfFileSegmentGenerator	byWholeContigSubdividingWithWidth(long segmentWidth)
static <T> VcfFileSegmentGenerator	excludingNonOverlaps(VcfFileSegmentGenerator strategy, htsjdk.samtools.util.OverlapDetector<T> overlaps) Returns a decorated VcfFileSegmentGenerator that filters out VcfFileSegments that have no overlap with the provided OverlapDetector.
abstract java.lang.Iterable<VcfFileSegment>	forVcf(java.io.File vcf)

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfFileSegmentGenerator

public VcfFileSegmentGenerator()

Method Detail

forVcf

public abstract java.lang.Iterable<VcfFileSegment> forVcf(java.io.File vcf)

byWholeContigSubdividingWithWidth

public static VcfFileSegmentGenerator byWholeContigSubdividingWithWidth(long segmentWidth)

excludingNonOverlaps

public static <T> VcfFileSegmentGenerator excludingNonOverlaps(VcfFileSegmentGenerator strategy,
                                                               htsjdk.samtools.util.OverlapDetector<T> overlaps)

Returns a decorated VcfFileSegmentGenerator that filters out VcfFileSegments that have no overlap with the provided OverlapDetector.