SnpSiftCmdRmInfo (SnpSift 5.4 API)

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdRmInfo

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

public class SnpSiftCmdRmInfo extends SnpSift

Removes INFO fields

Author:: pablocingolani

Field Summary

Fields inherited from class 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

SnpSiftCmdRmInfo()

SnpSiftCmdRmInfo(String[] args)
Method Summary

Modifier and Type

Method

Description

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Analyze the file

void

usage(String errMsg)

Show usage and exit

Methods inherited from class SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, init, 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 Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SnpSiftCmdRmInfo
  
  public SnpSiftCmdRmInfo()
- SnpSiftCmdRmInfo
  
  public SnpSiftCmdRmInfo(String[] args)
Method Details
- 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()
  
  Analyze the file
  
  Specified by:
  
  run in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  run in class SnpSift
- usage
  
  public void usage(String errMsg)
  
  Show usage and exit
  
  Specified by:
  
  usage in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  usage in class SnpSift