Class Pedigree

  • All Implemented Interfaces:
    java.lang.Iterable<PedigreeEntry>

    public class Pedigree
    extends java.lang.Object
    implements java.lang.Iterable<PedigreeEntry>
    A pedigree for cancer samples
    • Method Detail

      • 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 java.util.Set<Tuple<java.lang.Integer,​java.lang.Integer>> compareCancerGenotypes​(VcfEntry vcfEntry)
        Analyze which comparisons to make in cancer genomes
      • derived

        public java.util.List<PedigreeEntry> derived()
        A list of all derived pedigree entries
      • iterator

        public java.util.Iterator<PedigreeEntry> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<PedigreeEntry>
      • setDebug

        public void setDebug​(boolean debug)
      • setVerbose

        public void setVerbose​(boolean verbose)