org.seqdoop.hadoop_bam

Class LazyBCFGenotypesContext

java.lang.Object

htsjdk.variant.variantcontext.GenotypesContext

htsjdk.variant.variantcontext.LazyGenotypesContext

org.seqdoop.hadoop_bam.LazyParsingGenotypesContext

org.seqdoop.hadoop_bam.LazyBCFGenotypesContext

All Implemented Interfaces:

Serializable, Iterable<htsjdk.variant.variantcontext.Genotype>, Collection<htsjdk.variant.variantcontext.Genotype>, List<htsjdk.variant.variantcontext.Genotype>

public class LazyBCFGenotypesContext
extends LazyParsingGenotypesContext

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	LazyBCFGenotypesContext.HeaderDataCache
static class	LazyBCFGenotypesContext.Parser

Nested classes/interfaces inherited from class htsjdk.variant.variantcontext.LazyGenotypesContext

htsjdk.variant.variantcontext.LazyGenotypesContext.LazyData, htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser

Field Summary

Fields inherited from class htsjdk.variant.variantcontext.GenotypesContext

NO_GENOTYPES, notToBeDirectlyAccessedGenotypes, sampleNamesInOrder, sampleNameToOffset, serialVersionUID

Constructor Summary

Constructors

Constructor and Description
LazyBCFGenotypesContext(List<htsjdk.variant.variantcontext.Allele> alleles, int fields, byte[] unparsed, int count) Takes ownership of the given byte[]: don't modify its contents.

Method Summary

Methods inherited from class org.seqdoop.hadoop_bam.LazyParsingGenotypesContext

getParser

Methods inherited from class htsjdk.variant.variantcontext.LazyGenotypesContext

decode, ensureSampleNameMap, ensureSampleOrdering, getGenotypes, getUnparsedGenotypeData, invalidateSampleNameMap, invalidateSampleOrdering, isEmpty, size

Methods inherited from class htsjdk.variant.variantcontext.GenotypesContext

add, add, addAll, addAll, checkImmutability, clear, contains, containsAll, containsSample, containsSamples, copy, copy, create, create, create, create, create, get, get, getMaxPloidy, getSampleNames, getSampleNamesOrderedByName, immutable, indexOf, isLazyWithData, isMutable, iterateInSampleNameOrder, iterateInSampleNameOrder, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, replace, retainAll, set, subList, subsetToSamples, toArray, toArray, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.List

equals, hashCode, replaceAll, sort, spliterator

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

LazyBCFGenotypesContext

public LazyBCFGenotypesContext(List<htsjdk.variant.variantcontext.Allele> alleles,
                               int fields,
                               byte[] unparsed,
                               int count)

Takes ownership of the given byte[]: don't modify its contents.