Class PedFile

    • Field Detail

      • NO_PHENO

        public static final Number NO_PHENO
      • UNKNOWN_SEX

        public static final Sex UNKNOWN_SEX
    • Constructor Detail

      • PedFile

        public PedFile​(boolean isTabMode)
    • Method Detail

      • add

        public void add​(PedFile.PedTrio trio)
        Adds a trio to the PedFile keyed by the individual id.
      • write

        public void write​(File file)
        Writes a set of pedigrees out to disk.
      • fromFile

        public static PedFile fromFile​(File file,
                                       boolean isTabMode)
        Attempts to read a pedigree file into memory.
      • removeIncompleteTrios

        public PedFile removeIncompleteTrios()
        Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
      • fromSexMap

        public static PedFile fromSexMap​(Map<String,​Sex> sampleSexes)
        Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
        Parameters:
        sampleSexes - a map from sample-name to its sex
        Returns:
        a PedFile object that contains data.