Package Files

Class VCF


  • public class VCF
    extends java.lang.Object
    • Constructor Detail

      • VCF

        public VCF​(java.io.File f)
            throws java.io.FileNotFoundException,
                   java.io.IOException
        VCF code is all still very developmental and not documented! * Use at your own risk - it may not work as expected. *
        Throws:
        java.io.FileNotFoundException
        java.io.IOException
      • VCF

        public VCF​(Meta meta,
                   Data data)
    • Method Detail

      • writeFile

        public void writeFile​(java.io.File f)
                       throws java.io.FileNotFoundException,
                              java.io.IOException
        Throws:
        java.io.FileNotFoundException
        java.io.IOException
      • getMeta

        public Meta getMeta()
      • getData

        public Data getData()
      • stripInfo

        public void stripInfo()
      • removeInfo

        public void removeInfo​(java.lang.String s)
      • removeFormat

        public void removeFormat​(java.lang.String s)
      • clone

        public VCF clone()
      • fromDoubleArray

        public static VCF fromDoubleArray​(double[][] values,
                                          java.util.List<Position> positions,
                                          java.util.List<java.lang.String> samples,
                                          java.lang.String id,
                                          java.lang.String description)