Class Pedigree

java.lang.Object
org.snpeff.vcf.Pedigree
All Implemented Interfaces:
Iterable<PedigreeEntry>
public class Pedigree extends Object implements Iterable<PedigreeEntry>
A pedigree for cancer samples

  • Constructor Details

  • Method Details

    • anyBackToRef

      public boolean anyBackToRef(VcfEntry vcfEntry)
      Are there any "back to reference" cancer variant

    • anyDerived

      public boolean anyDerived()
      Is there any derived sample?

    • compareCancerGenotypes

      public Set<Tuple<Integer,Integer>> compareCancerGenotypes(VcfEntry vcfEntry)
      Analyze which comparisons to make in cancer genomes

    • derived

      public List<PedigreeEntry> derived()
      A list of all derived pedigree entries

    • iterator

      public Iterator<PedigreeEntry> iterator()
      Specified by:
      iterator in interface Iterable<PedigreeEntry>

    • setDebug

      public void setDebug(boolean debug)

    • setVerbose

      public void setVerbose(boolean verbose)