Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdBuild
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
- All Implemented Interfaces:
CommandLine
Command line program: Build database
- Author:
- pcingola
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Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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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, tags, tagsNo, testing, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
fileExists
(String path) Does either 'path' or 'path'+'.gz' exist?protected SnpEff.GeneDatabaseFormat
Try to guess database format by checking which file type is presentvoid
Parse command line argumentsboolean
run()
Build databasevoid
setCheckNumOk
(boolean checkNumOk) void
setStoreAlignments
(boolean storeAlignments) void
Show 'usage;' message and exit with an error code '-1'Methods inherited from class org.snpeff.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, setVerbose, usageDb, usageGeneric, usageGenericAndDb
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Constructor Details
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SnpEffCmdBuild
public SnpEffCmdBuild()
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Method Details
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fileExists
Does either 'path' or 'path'+'.gz' exist? -
getSnpEffCmdCds
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getSnpEffCmdProtein
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guessGenesFormat
Try to guess database format by checking which file type is present -
parseArgs
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) -
setStoreAlignments
public void setStoreAlignments(boolean storeAlignments) -
usage
Show 'usage;' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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