Package org.snpsift

Class SnpSiftCmdVcfOperator

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdVcfOperator
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdVcfOperator extends SnpSift
Annotate a field based on an operation (max, min, etc.) of other VCF fields
Author:
pcingola

  • Field Details

  • Constructor Details

    • SnpSiftCmdVcfOperator

      public SnpSiftCmdVcfOperator()

    • SnpSiftCmdVcfOperator

      public SnpSiftCmdVcfOperator(String[] args)

  • Method Details

    • annotate

      public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
      Specified by:
      annotate in interface org.snpeff.snpEffect.VcfAnnotator
      Overrides:
      annotate in class SnpSift

    • applyOp

      public Double applyOp(List<Double> vals)

    • getArgs

      public String[] getArgs()
      Specified by:
      getArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      getArgs in class SnpSift

    • getValues

      public List<Double> getValues(org.snpeff.vcf.VcfEntry vcfEntry)

    • getValues

      public List<Double> getValues(org.snpeff.vcf.VcfEntry vcfEntry, String field)
      Parse an INFO field (can be multiple valued) and return a list of Double

    • headers

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

    • initialValue

      protected double initialValue()

    • parseArgs

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

    • run

      public boolean run()
      Annotate
      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)
      Description copied from class: SnpSift
      Show usage message
      Specified by:
      usage in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      usage in class SnpSift