java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdLen

All Implemented Interfaces:: CommandLine

public class SnpEffCmdLen extends SnpEff

Calculate the maximum interval length by type, for all markers in a genome

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

SnpEffCmdLen()
Method Summary

Modifier and Type

Method

Description

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Run

void

usage(String message)

Show usage and exit

Methods inherited from class org.snpeff.SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, main, 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
- SnpEffCmdLen
  
  public SnpEffCmdLen()
Method Details
- 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()
  
  Run
  
  Specified by:
  
  run in interface CommandLine
  
  Overrides:
  
  run in class SnpEff
  
  Returns:
- usage
  
  public void usage(String message)
  
  Show usage and exit
  
  Specified by:
  
  usage in interface CommandLine
  
  Overrides:
  
  usage in class SnpEff

Class SnpEffCmdLen

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

SnpEffCmdLen

Method Details

parseArgs

run

usage