Package org.snpsift

Class SnpSiftCmdConcordance

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

    public class SnpSiftCmdConcordance
    extends SnpSift
    Calculate genotyping concordance between two VCF files. Typical usage: Calculate concordance between sequencing experiment and genotypting experiment.
    Author:
    pcingola
    • Constructor Detail

      • SnpSiftCmdConcordance

        public SnpSiftCmdConcordance()
      • SnpSiftCmdConcordance

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

      • getConcordance

        public org.snpeff.stats.CountByType getConcordance()
      • getConcordanceBySample

        public org.snpeff.collections.AutoHashMap<java.lang.String,​org.snpeff.stats.CountByType> getConcordanceBySample()
      • getCountEntries

        public int getCountEntries()
      • init

        public void init()
        Description copied from class: SnpSift
        Initialize default values
        Overrides:
        init in class SnpSift
      • 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
      • run

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

        public void setWriteBySampleFile​(boolean writeBySampleFile)
      • setWriteSummaryFile

        public void setWriteSummaryFile​(boolean writeSummaryFile)
      • 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