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

Field Summary

Fields inherited from class org.snpsift.SnpSift
args, BUILD, command, config, configFile, dataDir, dbFileName, dbTabix, dbType, debug, download, EMPTY_ARGS, errCount, genomeVersion, help, log, needsConfig, needsDb, needsGenome, numWorkers, output, quiet, REVISION, saveOutput, shiftArgs, SHOW_EVERY_VCFLINES, showVcfHeader, showVersion, SOFTWARE_NAME, suppressOutput, vcfHeaderAddProgramVersion, vcfHeaderProcessed, vcfInputFile, verbose, VERSION, VERSION_MAJOR, VERSION_NO_NAME, VERSION_SHORT
Constructor Summary

Constructors

Constructor

Description

SnpSiftCmdIntervalsIndex()

SnpSiftCmdIntervalsIndex(String[] args)
Method Summary

Modifier and Type

Method

Description

void

init()

Initialize default values

void

loadIntervals()

Load all BED files

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Load a file compare calls

void

setInOffset(int inOffset)

void

usage(String msg)

Show usage message

Methods inherited from class org.snpsift.SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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 -

Class SnpSiftCmdIntervalsIndex

Field Summary

Fields inherited from class org.snpsift.SnpSift

Constructor Summary

Method Summary

Methods inherited from class org.snpsift.SnpSift

Methods inherited from class java.lang.Object

Constructor Details

SnpSiftCmdIntervalsIndex

SnpSiftCmdIntervalsIndex

Method Details

init

loadIntervals

parseArgs

run

setInOffset

usage