org.seqdoop.hadoop_bam

Class VariantContextWithHeader

java.lang.Object

htsjdk.variant.variantcontext.VariantContext

org.seqdoop.hadoop_bam.VariantContextWithHeader

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, htsjdk.tribble.Feature, Serializable

public class VariantContextWithHeader
extends htsjdk.variant.variantcontext.VariantContext

See Also:

Serialized Form

Nested Class Summary

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

htsjdk.variant.variantcontext.VariantContext.Type, htsjdk.variant.variantcontext.VariantContext.Validation

Field Summary

Fields inherited from class htsjdk.variant.variantcontext.VariantContext

alleles, commonInfo, contig, genotypeCounts, genotypes, NO_GENOTYPES, NO_LOG10_PERROR, PASSES_FILTERS, serialVersionUID, start, stop, type

Constructor Summary

Constructors

Constructor and Description
VariantContextWithHeader(htsjdk.variant.variantcontext.VariantContext context, htsjdk.variant.vcf.VCFHeader header)

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.vcf.VCFHeader	getHeader()

Methods inherited from class htsjdk.variant.variantcontext.VariantContext

calcVCFGenotypeKeys, emptyID, extraStrictValidation, filtersWereApplied, fullyDecode, getAllele, getAllele, getAlleleIndex, getAlleleIndices, getAlleles, getAltAlleleWithHighestAlleleCount, getAlternateAllele, getAlternateAlleles, getAttribute, getAttribute, getAttributeAsBoolean, getAttributeAsDouble, getAttributeAsDoubleList, getAttributeAsInt, getAttributeAsIntList, getAttributeAsList, getAttributeAsString, getAttributeAsStringList, getAttributes, getCalledChrCount, getCalledChrCount, getCalledChrCount, getCalledChrCount, getCommonInfo, getContig, getEnd, getFilters, getFiltersMaybeNull, getGenotype, getGenotype, getGenotypes, getGenotypes, getGenotypes, getGenotypes, getGenotypesOrderedBy, getGenotypesOrderedByName, getGLIndecesOfAlternateAllele, getHetCount, getHomRefCount, getHomVarCount, getID, getIndelLengths, getLog10PError, getMaxPloidy, getMixedCount, getNAlleles, getNoCallCount, getNSamples, getPhredScaledQual, getReference, getSampleNames, getSampleNamesOrderedByName, getSource, getStart, getStructuralVariantType, getType, hasAllele, hasAllele, hasAlternateAllele, hasAlternateAllele, hasAttribute, hasGenotype, hasGenotypes, hasGenotypes, hasID, hasLog10PError, hasSameAllelesAs, hasSameAlternateAllelesAs, hasSymbolicAlleles, hasSymbolicAlleles, isBiallelic, isComplexIndel, isFiltered, isFullyDecoded, isIndel, isMixed, isMNP, isMonomorphicInSamples, isNotFiltered, isPointEvent, isPolymorphicInSamples, isSimpleDeletion, isSimpleIndel, isSimpleInsertion, isSNP, isStructuralIndel, isSymbolic, isSymbolicOrSV, isVariant, subContextFromSample, subContextFromSamples, subContextFromSamples, toString, toStringDecodeGenotypes, toStringWithoutGenotypes, validateAlternateAlleles, validateChromosomeCounts, validateReferenceBases, validateRSIDs

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.tribble.Feature

getChr

Constructor Detail

VariantContextWithHeader

public VariantContextWithHeader(htsjdk.variant.variantcontext.VariantContext context,
                                htsjdk.variant.vcf.VCFHeader header)

Method Detail

getHeader

public htsjdk.variant.vcf.VCFHeader getHeader()