Package picard.vcf.processor
Class VcfFileSegmentGenerator
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- picard.vcf.processor.VcfFileSegmentGenerator
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@Deprecated public abstract class VcfFileSegmentGenerator extends Object
Deprecated.from 2022-03-17, UseVcfPathSegmentGenerator
Describes a mechanism for producingVcfFileSegment
s from a VCF file.
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Constructor Summary
Constructors Constructor Description VcfFileSegmentGenerator()
Deprecated.
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods 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 decoratedVcfFileSegmentGenerator
that filters outVcfFileSegment
s that have no overlap with the providedOverlapDetector
.abstract Iterable<VcfFileSegment>
forVcf(File vcf)
Deprecated.
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Method Detail
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forVcf
public abstract Iterable<VcfFileSegment> forVcf(File vcf)
Deprecated.
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byWholeContigSubdividingWithWidth
public static VcfFileSegmentGenerator byWholeContigSubdividingWithWidth(long segmentWidth)
Deprecated.
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excludingNonOverlaps
public static <T> VcfFileSegmentGenerator excludingNonOverlaps(VcfFileSegmentGenerator strategy, htsjdk.samtools.util.OverlapDetector<T> overlaps)
Deprecated.Returns a decoratedVcfFileSegmentGenerator
that filters outVcfFileSegment
s that have no overlap with the providedOverlapDetector
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