Hierarchy For Package picard.vcf

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • picard.vcf.ByIntervalListVariantContextIterator (implements java.util.Iterator<E>)
  • picard.vcf.CallingMetricAccumulator (implements picard.vcf.processor.VariantProcessor.Accumulator<RESULT>)
    • picard.vcf.GvcfMetricAccumulator
  • picard.vcf.CallingMetricAccumulator.Result
  • picard.cmdline.CommandLineProgram
    • picard.vcf.AccumulateVariantCallingMetrics
    • picard.vcf.CollectVariantCallingMetrics
    • picard.vcf.FixVcfHeader
    • picard.vcf.GatherVcfs
    • picard.vcf.GenotypeConcordance
    • picard.vcf.LiftoverVcf
    • picard.vcf.MakeSitesOnlyVcf
    • picard.vcf.MakeVcfSampleNameMap
    • picard.vcf.MergeVcfs
    • picard.vcf.RenameSampleInVcf
    • picard.vcf.SortVcf
    • picard.vcf.SplitVcfs
    • picard.vcf.UpdateVcfSequenceDictionary
    • picard.vcf.VcfFormatConverter
    • picard.vcf.VcfToIntervalList
  • picard.vcf.GenotypeConcordance.Alleles
  • picard.vcf.GenotypeConcordanceCounts
  • picard.vcf.GenotypeConcordanceScheme
    • picard.vcf.GA4GHScheme
    • picard.vcf.GA4GHSchemeWithMissingAsHomRef
  • picard.vcf.GenotypeConcordanceSchemeFactory
  • picard.vcf.GenotypeConcordanceStates
  • picard.vcf.GenotypeConcordanceStates.TruthAndCallStates (implements java.lang.Comparable<T>)
  • htsjdk.samtools.metrics.MetricBase
    • picard.vcf.GenotypeConcordanceContingencyMetrics
    • picard.vcf.GenotypeConcordanceDetailMetrics
    • picard.vcf.GenotypeConcordanceSummaryMetrics
    • picard.analysis.MergeableMetricBase
      • picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
        • picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
  • picard.vcf.PairedVariantSubContextIterator (implements java.util.Iterator<E>)
  • picard.vcf.PairedVariantSubContextIterator.VcfTuple
  • picard.vcf.VcfUtils

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • picard.vcf.GenotypeConcordanceStates.ContingencyState
    • picard.vcf.GenotypeConcordanceStates.CallState
    • picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
    • picard.vcf.GenotypeConcordanceStates.TruthState
    • picard.vcf.GenotypeConcordanceStateCodes