Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdCount
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdCount
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdCount extends SnpEff
Count reads from a BAM file given a list of intervals- Author:
- pablocingolani
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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 SnpEffCmdCount()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
parseArgs(java.lang.String[] args)
Parseboolean
run()
Runvoid
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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parseArgs
public void parseArgs(java.lang.String[] args)
Parse- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
- Parameters:
args
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run
public boolean run()
Run- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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usage
public void usage(java.lang.String message)
Description copied from class:SnpEff
Show 'usage' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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