Package org.snpsift

Class SnpSiftCmdFilterGt

java.lang.Object
org.snpsift.SnpSift
org.snpsift.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 invalid input: '<' 20", all genotypes with quality lower than 20 will be replaced by './.' (missing)
Author:
pablocingolani

  • Constructor Details

    • SnpSiftCmdFilterGt

      public SnpSiftCmdFilterGt()

    • SnpSiftCmdFilterGt

      public SnpSiftCmdFilterGt(String[] args)

  • Method Details

    • addSet

      public void addSet(String fileName)
      Read a file as a string set

    • filter

      public List<org.snpeff.vcf.VcfEntry> filter(String fileName, String expression, boolean createList)
      Filter a file

    • headers

      protected 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(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(String expression) throws Exception
      Parse expression
      Throws:
      Exception

    • 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