Class PedigreeEntry

java.lang.Object
org.snpeff.vcf.PedigreeEntry

public class PedigreeEntry extends Object
Pedigree entry in a VCF file header E.g.: ##PEDIGREE=invalid input: '<'Derived=Patient_01_Somatic,Original=Patient_01_Germline> or ##PEDIGREE=invalid input: '<'Child=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>
Author:
pcingola
  • Field Details

    • father

      public String father
    • mother

      public String mother
    • child

      public String child
    • fatherNum

      public int fatherNum
    • motherNum

      public int motherNum
    • childNum

      public int childNum
  • Constructor Details

    • PedigreeEntry

      public PedigreeEntry(String original, String derived)
    • PedigreeEntry

      public PedigreeEntry(String father, String mother, String child)
  • Method Details

    • getDerived

      public String getDerived()
    • getDerivedNum

      public int getDerivedNum()
    • getOriginal

      public String getOriginal()
    • getOriginalNum

      public int getOriginalNum()
    • isDerived

      public boolean isDerived()
      Is this an 'Original-Derived' entry type?
      Returns:
    • sampleNumbers

      public void sampleNumbers(List<String> sampleNames)
      Find sample numbers in a list of sample names
      Parameters:
      sampleNames -
    • toString

      public String toString()
      Overrides:
      toString in class Object