org.seqdoop.hadoop_bam

Class LazyParsingGenotypesContext

java.lang.Object

htsjdk.variant.variantcontext.GenotypesContext

htsjdk.variant.variantcontext.LazyGenotypesContext

org.seqdoop.hadoop_bam.LazyParsingGenotypesContext

All Implemented Interfaces:

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

Direct Known Subclasses:

LazyBCFGenotypesContext, LazyVCFGenotypesContext

public abstract class LazyParsingGenotypesContext
extends htsjdk.variant.variantcontext.LazyGenotypesContext

You need to call getParser().setHeader() here before trying to decode() a GenotypesContext in any VariantContext that came about via VariantContextWritable.readFields(). That includes calling VariantContext.fullyDecode() or almost any of the GenotypesContext methods. The RecordReader provided by VCFInputFormat does this for you.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	LazyParsingGenotypesContext.HeaderDataCache
static class	LazyParsingGenotypesContext.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

Modifier	Constructor and Description
protected	LazyParsingGenotypesContext(LazyParsingGenotypesContext.Parser p, byte[] data, int count)

Method Summary

Modifier and Type	Method and Description
LazyParsingGenotypesContext.Parser	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

LazyParsingGenotypesContext

protected LazyParsingGenotypesContext(LazyParsingGenotypesContext.Parser p,
                                      byte[] data,
                                      int count)

Method Detail

getParser

public LazyParsingGenotypesContext.Parser getParser()