java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed

All Implemented Interfaces:: CommandLine

public class SnpEffCmdGenes2Bed extends SnpEff

Simple test program

Author:: pcingola

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
Field Summary

Fields inherited from class org.snpeff.SnpEff
args, BUILD, BUILD_DATE, canonical, canonicalFile, command, COMMAND_LINE_WIDTH, config, configFile, configOverride, customIntervalFiles, dataDir, debug, DEFAULT_COMMAND, download, expandIub, filterIntervalFiles, genome, genomeVer, help, hgvs, hgvsForce, hgvsOld, hgvsOneLetterAa, hgvsShift, hgvsTrId, interaction, log, maxTranscriptSupportLevel, motif, multiThreaded, nextProt, nextProtKeepAllTrs, noGenome, numWorkers, onlyProtein, onlyRegulation, onlyTranscriptsFile, output, quiet, regulationTracks, REVISION, saveOutput, shiftArgs, snpEffCmd, SOFTWARE_NAME, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, spliceSiteSize, strict, suppressOutput, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
Constructor Summary

Constructors

Constructor

Description

SnpEffCmdGenes2Bed()
Method Summary

Modifier and Type

Method

Description

static void

main(String[] args)

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Run according to command line options

void

showGenes()

Show genes in BED format

void

usage(String message)

Show 'usage' message and exit with an error code '-1'

Methods inherited from class org.snpeff.SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, reportValues, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb

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

Constructor Details
- SnpEffCmdGenes2Bed
  
  public SnpEffCmdGenes2Bed()
Method Details
- main
  
  public static void main(String[] args)
- parseArgs
  
  public void parseArgs(String[] args)
  
  Description copied from class: SnpEff
  
  Parse command line arguments
  
  Specified by:
  
  parseArgs in interface CommandLine
  
  Overrides:
  
  parseArgs in class SnpEff
- run
  
  public boolean run()
  
  Description copied from class: SnpEff
  
  Run according to command line options
  
  Specified by:
  
  run in interface CommandLine
  
  Overrides:
  
  run in class SnpEff
- showGenes
  
  public void showGenes()
  
  Show genes in BED format
- usage
  
  public void usage(String message)
  
  Description copied from class: SnpEff
  
  Show 'usage' message and exit with an error code '-1'
  
  Specified by:
  
  usage in interface CommandLine
  
  Overrides:
  
  usage in class SnpEff

Class SnpEffCmdGenes2Bed

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.SnpEff

Field Summary

Fields inherited from class org.snpeff.SnpEff

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.SnpEff

Methods inherited from class java.lang.Object

Constructor Details

SnpEffCmdGenes2Bed

Method Details

main

parseArgs

run

showGenes

usage