java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdClosest

All Implemented Interfaces:: CommandLine

public class SnpEffCmdClosest extends SnpEff

Command line: Find closes marker to each variant

Author:: pcingola

Nested Class Summary

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

Fields

Modifier and Type

Field

Description

static final String

CLOSEST

static final String

INFO_LINE

Fields inherited from class 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, tags, tagsNo, testing, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
Constructor Summary

Constructors

Constructor

Description

SnpEffCmdClosest()

SnpEffCmdClosest(Config config)
Method Summary

Modifier and Type

Method

Description

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Run command

void

setVerbose(boolean verbose)

void

usage(String message)

Show usage and exit

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

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

Field Details
- CLOSEST
  public static final String CLOSEST
  
  See Also:
  
  Constant Field Values
- INFO_LINE
  public static final String INFO_LINE
  
  See Also:
  
  Constant Field Values
Constructor Details
- SnpEffCmdClosest
  
  public SnpEffCmdClosest()
- SnpEffCmdClosest
  
  public SnpEffCmdClosest(Config config)
Method Details
- parseArgs
  
  public void parseArgs(String[] args)
  
  Parse command line arguments
  
  Specified by:
  
  parseArgs in interface CommandLine
  
  Overrides:
  
  parseArgs in class SnpEff
- run
  
  public boolean run()
  
  Run command
  
  Specified by:
  
  run in interface CommandLine
  
  Overrides:
  
  run in class SnpEff
- setVerbose
  
  public void setVerbose(boolean verbose)
  
  Overrides:
  
  setVerbose in class SnpEff
- usage
  
  public void usage(String message)
  
  Show usage and exit
  
  Specified by:
  
  usage in interface CommandLine
  
  Overrides:
  
  usage in class SnpEff

Class SnpEffCmdClosest

Nested Class Summary

Nested classes/interfaces inherited from class SnpEff

Field Summary

Fields inherited from class SnpEff

Constructor Summary

Method Summary

Methods inherited from class SnpEff

Methods inherited from class Object

Field Details

CLOSEST

INFO_LINE

Constructor Details

SnpEffCmdClosest

SnpEffCmdClosest

Method Details

parseArgs

run

setVerbose

usage