Class SnpEffCmdCount
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdCount
- All Implemented Interfaces:
CommandLine
Count reads from a BAM file given a list of intervals
- Author:
- pablocingolani
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Nested Class Summary
Nested classes/interfaces inherited from class SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat -
Field Summary
Fields inherited from class 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 -
Constructor Summary
Constructors -
Method Summary
Methods inherited from class 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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SnpEffCmdCount
public SnpEffCmdCount()
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Method Details
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parseArgs
Parse- Specified by:
parseArgsin interfaceCommandLine- Overrides:
parseArgsin classSnpEff- Parameters:
args-
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run
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usage
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