VcfFileSegmentGenerator (picard 3.4.0 API)

java.lang.Object

picard.vcf.processor.VcfFileSegmentGenerator

@Deprecated public abstract class VcfFileSegmentGenerator extends Object

Deprecated.

from 2022-03-17, Use VcfPathSegmentGenerator

Describes a mechanism for producing VcfFileSegments from a VCF file.

Constructor Summary

Constructors

Constructor

Description

VcfFileSegmentGenerator()

Deprecated.
Method Summary

Modifier and Type

Method

Description

static VcfFileSegmentGenerator

byWholeContigSubdividingWithWidth(long segmentWidth)

Deprecated.

static <T> VcfFileSegmentGenerator

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

Deprecated.

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

abstract Iterable<VcfFileSegment>

forVcf(File vcf)

Deprecated.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- VcfFileSegmentGenerator
  
  public VcfFileSegmentGenerator()
  
  Deprecated.
Method Details
- forVcf
  
  public abstract Iterable<VcfFileSegment> forVcf(File vcf)
  
  Deprecated.
- byWholeContigSubdividingWithWidth
  
  public static VcfFileSegmentGenerator byWholeContigSubdividingWithWidth(long segmentWidth)
  
  Deprecated.
- excludingNonOverlaps
  
  public static <T> VcfFileSegmentGenerator excludingNonOverlaps(VcfFileSegmentGenerator strategy, htsjdk.samtools.util.OverlapDetector<T> overlaps)
  
  Deprecated.
  
  Returns a decorated VcfFileSegmentGenerator that filters out VcfFileSegments that have no overlap with the provided OverlapDetector.