SnpEffCmdBuild (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.SnpEff
- - org.snpeff.snpEffect.commandLine.SnpEffCmdBuild

All Implemented Interfaces:

CommandLine
```
public class SnpEffCmdBuild
extends SnpEff
```
Command line program: Build database

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

SnpEffCmdBuild()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`fileExists(java.lang.String path)`	Does either 'path' or 'path'+'.gz' exist?
`SnpEffCmdCds`	`getSnpEffCmdCds()`
`SnpEffCmdProtein`	`getSnpEffCmdProtein()`
`protected SnpEff.GeneDatabaseFormat`	`guessGenesFormat()`	Try to guess database format by checking which file type is present
`void`	`parseArgs(java.lang.String[] args)`	Parse command line arguments
`boolean`	`run()`	Build database
`void`	`setCheckNumOk(boolean checkNumOk)`
`void`	`setStoreAlignments(boolean storeAlignments)`
`void`	`usage(java.lang.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, 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 Detail
  - SnpEffCmdBuild
```
public SnpEffCmdBuild()
```
- Method Detail
  - fileExists
```
protected boolean fileExists(java.lang.String path)
```
    Does either 'path' or 'path'+'.gz' exist?
  - getSnpEffCmdCds
```
public SnpEffCmdCds getSnpEffCmdCds()
```
  - getSnpEffCmdProtein
```
public SnpEffCmdProtein getSnpEffCmdProtein()
```
  - guessGenesFormat
```
protected SnpEff.GeneDatabaseFormat guessGenesFormat()
```
    Try to guess database format by checking which file type is present
  - 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()
```
    Build database
    
    Specified by:
    
    run in interface CommandLine
    
    Overrides:
    
    run in class SnpEff
  - setCheckNumOk
```
public void setCheckNumOk(boolean checkNumOk)
```
  - setStoreAlignments
```
public void setStoreAlignments(boolean storeAlignments)
```
  - usage
```
public void usage(java.lang.String message)
```
    Show 'usage;' message and exit with an error code '-1'
    
    Specified by:
    
    usage in interface CommandLine
    
    Overrides:
    
    usage in class SnpEff