Constructor Detail

• HaplotypeNode

  HaplotypeNode(HaplotypeSequence haplotypeSequence, TaxaList taxaList, int id, String asmContig, int asmStart, int asmEnd, String asmStrand, int genomeFileID, int gvcfFileID)

  Constructor

  Parameters:

  haplotypeSequence - sequence

  taxaList - taxa list

  id - hapid from database

  asmContig - assembly contig / chromosome

  asmStart - assembly start coordinate

  asmEnd - assembly end coordinate

  genomeFileID - genome file ID

  gvcfFileID - gvcf file ID

• HaplotypeNode

  HaplotypeNode(HaplotypeSequence haplotypeSequence, TaxaList taxaList, int id)

• HaplotypeNode

  HaplotypeNode(HaplotypeSequence haplotypeSequence, TaxaList taxaList)

Method Detail

• haplotypeSequence

   HaplotypeSequence haplotypeSequence()

  HaplotypeSequence object containing the nucleotide sequence and other sequence related information for a given HaplotypeNode object.

• taxaList

   TaxaList taxaList()

  List of taxa used when the consensus sequence was created or a single taxon.

• id

   int id()

• asmContig

   String asmContig()

• asmStart

   int asmStart()

• asmEnd

   int asmEnd()

• asmStrand

   String asmStrand()

• genomeFileID

   int genomeFileID()

• gvcfFileID

   int gvcfFileID()

• referenceRange

   ReferenceRange referenceRange()

  Object containing the range of genomic coordinate values associated with a given HaplotypeNode and other details associated with that range of values. These values correspond to the reference genome being used (Generally B73 in Maize).

• numTaxa

   int numTaxa()

  Number of taxa used when consensus sequence was created or one if this is an original sequence.

• toString

   String toString()

• variantInfos

   Optional<List<HaplotypeNode.VariantInfo>> variantInfos()

  These correspond to the VariantContext but holds less information for memory efficiency. For reference blocks, isVariant will be false and refAllele may equal "REF" rather than the actual allele for the first base pair of the block. For that reason, converting VariantInfo to VariantContext will require a copy of the reference genome sequence to get the actual refAllele values.

• compareTo

   int compareTo(HaplotypeNode o)

• variantContexts

   Optional<List<VariantContext>> variantContexts()