Package org.snpsift

Class SnpSiftCmdFilterGt

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

    public class SnpSiftCmdFilterGt
    extends SnpSift
    Generic SnpSift genotype filter Removes genotypes matching the filter: e.g. if the expression is "GQ < 20", all genotypes with quality lower than 20 will be replaced by './.' (missing)
    Author:
    pablocingolani
    • Constructor Detail

      • SnpSiftCmdFilterGt

        public SnpSiftCmdFilterGt()
      • SnpSiftCmdFilterGt

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

      • addSet

        public void addSet​(java.lang.String fileName)
        Read a file as a string set
      • filter

        public java.util.List<org.snpeff.vcf.VcfEntry> filter​(java.lang.String fileName,
                                                              java.lang.String expression,
                                                              boolean createList)
        Filter a file
      • headers

        protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
        Description copied from class: SnpSift
        Headers to add
        Overrides:
        headers in class SnpSift
      • init

        public void init()
        Initialize default values
        Overrides:
        init in class SnpSift
      • 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
      • parseExpression

        public Expression parseExpression​(java.lang.String expression)
                                   throws java.lang.Exception
        Parse expression
        Throws:
        java.lang.Exception
      • 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