SnpEffCmdClosest (SnpEff 5.1 API)

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 org.snpeff.SnpEff
  SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat

Field Summary

Fields
Modifier and Type Field Description

static java.lang.String CLOSEST

static java.lang.String INFO_LINE
- 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

SnpEffCmdClosest()

SnpEffCmdClosest(Config config)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`parseArgs(java.lang.String[] args)`	Parse command line arguments
`boolean`	`run()`	Run command
`void`	`setVerbose(boolean verbose)`
`void`	`usage(java.lang.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, usageDb, usageGeneric, usageGenericAndDb

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

- Field Detail
  - CLOSEST
```
public static final java.lang.String CLOSEST
```
    See Also:
    
    Constant Field Values
  - INFO_LINE
```
public static final java.lang.String INFO_LINE
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SnpEffCmdClosest
```
public SnpEffCmdClosest()
```
  - SnpEffCmdClosest
```
public SnpEffCmdClosest(Config config)
```
- Method Detail
  - parseArgs
```
public void parseArgs(java.lang.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(java.lang.String message)
```
    Show usage and exit
    
    Specified by:
    
    usage in interface CommandLine
    
    Overrides:
    
    usage in class SnpEff