SnpSiftCmdVcfCheck (SnpSift 5.4 API)

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdVcfCheck

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

public class SnpSiftCmdVcfCheck extends SnpSift

Check VCF files (run some simple checks)

Author:: pcingola

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

SnpSiftCmdVcfCheck()

SnpSiftCmdVcfCheck(String[] args)
Method Summary

Modifier and Type

Method

Description

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Process the whole VCF file

void

usage(String msg)

Show usage message

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
- SnpSiftCmdVcfCheck
  
  public SnpSiftCmdVcfCheck()
- SnpSiftCmdVcfCheck
  
  public SnpSiftCmdVcfCheck(String[] args)
Method Details
- 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
- run
  
  public boolean run()
  
  Process the whole VCF file
  
  Specified by:
  
  run in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  run in class SnpSift
- 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 -