Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdBuild
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdBuild extends SnpEff
Command line program: Build database- Author:
- pcingola
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Nested Class Summary
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Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description SnpEffCmdBuild()
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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 presentvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Build databasevoid
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, error, fatalError, 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, warning
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Method Detail
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fileExists
protected boolean fileExists(java.lang.String path)
Does either 'path' or 'path'+'.gz' exist?
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getSnpEffCmdCds
public SnpEffCmdCds getSnpEffCmdCds()
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getSnpEffCmdProtein
public SnpEffCmdProtein getSnpEffCmdProtein()
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guessGenesFormat
protected SnpEff.GeneDatabaseFormat guessGenesFormat()
Try to guess database format by checking which file type is present
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
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run
public boolean run()
Build database- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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setCheckNumOk
public void setCheckNumOk(boolean checkNumOk)
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setStoreAlignments
public void setStoreAlignments(boolean storeAlignments)
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usage
public void usage(java.lang.String message)
Show 'usage;' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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