Constructor Detail

Method Detail

• getVariantContextFromHaplotypePath

   static List<VariantContext> getVariantContextFromHaplotypePath(HaplotypePath bestPath)

  Method to extract the VCF VariantContexts from the HaplotypePath. TODO remove if we get rid of HaplotypePath

  Parameters:

  bestPath - HaplotypePath containing one single path through the PHG.

• getVariantContextFromHaplotypeNodeList

   static List<VariantContext> getVariantContextFromHaplotypeNodeList(List<HaplotypeNode> nodeList)

  Method to extract the VCF VariantContexts from a List of HaplotypeNodes

  Parameters:

  nodeList - List of HaplotypeNodes which we want the variantContexts from

• writeVariantContextsToVCF

   static void writeVariantContextsToVCF(List<VariantContext> variantContextList, String exportVCFFileName, String referenceFileName, List<String> taxa)

• writeVariantContextsToVCF

   static void writeVariantContextsToVCF(List<VariantContext> variantContextList, String exportVCFFileName, String referenceFileName, String taxonName)

  Method to write the list of VariantContexts out to a vcf file. If the referenceFileName is not null, it will also index the file on the fly. TODO when we convert TASSEL's VCF reader to use htsjdk, rework this method into ExportUtils TODO use an optional for the referenceFileName

  Parameters:

  variantContextList - list of VariantContext objects that need to be written to the vcf file

  exportVCFFileName - String file name of the exported VCF file

  referenceFileName - String name of the reference fasta file name.

  taxonName - Taxon name

• callSNPsFromHaplotypePath

   static void callSNPsFromHaplotypePath(HaplotypeGraph graph, HaplotypePath bestPath, String vcfFileDir, String exportVCFFileName, String referenceFileName, String taxonName)

• callSNPsFromSomeVCFs

   static void callSNPsFromSomeVCFs(String inputVCFFileDir, String exportVCFFileName, String referenceFileName, String taxonName)

• callSNPsFromHaplotypeNodes

   static void callSNPsFromHaplotypeNodes(List<HaplotypeNode> listOfNodes, HashMap<Integer, String> hapIdToFileNameMapping, String vcfFileDir, String exportVCFFileName, String referenceFileName, String taxonName)

• createHapIdToFileNameMapping

   static HashMap<Integer, String> createHapIdToFileNameMapping(HaplotypeGraph graph, String pangenomeDir)

• createGenericHeader

   static VCFHeader createGenericHeader(List<String> taxaNames)

• createGenericHeaderLineSet

   static Set<VCFHeaderLine> createGenericHeaderLineSet()

• createGATKGVCFHeader

   static VCFHeader createGATKGVCFHeader(List<String> taxaNames)

• addInGQBlockHeader

   static void addInGQBlockHeader(Set<VCFHeaderLine> headerLines)

• createGVCFBlockHeaderLine

   static VCFHeaderLine createGVCFBlockHeaderLine(int start, int exclusiveEnd)