Class VcfOutputFormatter


  • public class VcfOutputFormatter
    extends OutputFormatter
    Formats output as VCF
    Author:
    pcingola
    • Field Detail

      • debug

        public static boolean debug
      • VCF_INFO_OICR_NAME

        public static final java.lang.String VCF_INFO_OICR_NAME
        See Also:
        Constant Field Values
    • Constructor Detail

      • VcfOutputFormatter

        public VcfOutputFormatter()
      • VcfOutputFormatter

        public VcfOutputFormatter​(java.util.List<VcfEntry> vcfEntries)
        Add all vcf entries to a list (used only for debugging and test-cases)
    • Method Detail

      • addHeader

        protected void addHeader()
        Add header
      • addInfo

        protected void addInfo​(VcfEntry vcfEntry)
        Add effects to INFO field
      • getNewHeaderLines

        public java.util.List<java.lang.String> getNewHeaderLines()
        New lines to be added to header
      • setFormatVersion

        public void setFormatVersion​(EffFormatVersion formatVersion)
      • setGatk

        public void setGatk​(boolean gatk)
      • setLossOfFunction

        public void setLossOfFunction​(boolean lossOfFunction)