Package org.snpsift

Class 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 Detail

      • SnpSiftCmdFilterChrPos

        public SnpSiftCmdFilterChrPos()
      • SnpSiftCmdFilterChrPos

        public SnpSiftCmdFilterChrPos​(java.lang.String[] args)
    • Method Detail

      • 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​(java.lang.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 java.util.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​(java.lang.String msg)
        Usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift