Class SnpSiftCmdIntervalsIndex

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdIntervalsIndex
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdIntervalsIndex extends SnpSift
Filter variants that hit intervals Use an indexed VCF file. WARNIGN: File must be uncompressed
Author:
pablocingolani

  • Constructor Details

    • SnpSiftCmdIntervalsIndex

      public SnpSiftCmdIntervalsIndex()

    • SnpSiftCmdIntervalsIndex

      public SnpSiftCmdIntervalsIndex(String[] args)

  • Method Details

    • init

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

    • loadIntervals

      public void loadIntervals()
      Load all BED files
      Parameters:
      bedFileNames -

    • parseArgs

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

    • run

      public boolean run()
      Load a file compare calls
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift
      Parameters:
      fileName -

    • setInOffset

      public void setInOffset(int inOffset)

    • usage

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