Package org.snpsift

Class SnpSiftCmdFilterChrPos

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdFilterChrPos
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdFilterChrPos extends SnpSift
Filter using CHROM:POS only
Author:
pablocingolani
  • Constructor Details

    • SnpSiftCmdFilterChrPos

      public SnpSiftCmdFilterChrPos()
    • SnpSiftCmdFilterChrPos

      public SnpSiftCmdFilterChrPos(String[] args)
  • Method Details

    • filter

      protected boolean filter(org.snpeff.vcf.VcfEntry vcfEntry)
      Filter this line?
      Returns:
      true if the filter is satisfied, false otherwise
    • parseArgs

      public void parseArgs(String[] args)
      Parse command line options
      Specified by:
      parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      parseArgs in class SnpSift
    • run

      public boolean run()
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift
    • run

      public List<org.snpeff.vcf.VcfEntry> run(boolean createList)
      Run filter
      Parameters:
      createList - : If true, create a list with the results. If false, show results on STDOUT
      Returns:
      If 'createList' is true, return a list containing all vcfEntries that passed the filter. Otherwise return null.
    • usage

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