Class SnpSiftCmdAlleleMatrix

java.lang.Object
org.snpsift.SnpSift
org.snpsift.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 Details

    • SEPARATOR

      public static String SEPARATOR

    • SHOW_EVERY

      public static int SHOW_EVERY

  • Constructor Details

    • SnpSiftCmdAlleleMatrix

      public SnpSiftCmdAlleleMatrix()

  • Method Details

    • parseArgs

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