Package org.snpsift

Class SnpSiftCmdAlleleMatrix

  • All Implemented Interfaces:
    org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

    public class SnpSiftCmdAlleleMatrix
    extends SnpSift
    Convert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles. I.e. the matrix has three possible values in each cell: - 0, for allele 0/0 - 1, for allele 0/1 or 1/0 - 2, for allele 1/1
    Author:
    pcingola
    • Field Detail

      • SEPARATOR

        public static java.lang.String SEPARATOR
      • SHOW_EVERY

        public static int SHOW_EVERY
    • Constructor Detail

      • SnpSiftCmdAlleleMatrix

        public SnpSiftCmdAlleleMatrix()
    • Method Detail

      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Parse command line arguments
        Specified by:
        parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        parseArgs in class SnpSift
      • processStr

        public int processStr​(org.snpeff.vcf.VcfEntry vcfEntry,
                              java.lang.StringBuilder sbcodes)
        Process a VCF entry and return a string (tab separated values)
      • run

        public boolean run()
        Process the whole VCF file
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift
      • usage

        public void usage​(java.lang.String msg)
        Show usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift