Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdCds
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdCds
- All Implemented Interfaces:
CommandLine
Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures
Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.
- 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
FieldsModifier and TypeFieldDescriptionstatic int
static double
static boolean
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
ConstructorsConstructorDescriptionSnpEffCmdCds
(String genomeVer, String configFile, String cdsFile) SnpEffCmdCds
(Config config) -
Method Summary
Modifier and TypeMethodDescriptionvoid
Parse command line argumentsboolean
run()
Run commandvoid
setCheckNumOk
(boolean checkNumOk) void
setMaxErrorRate
(double maxErrorRate) void
setStoreAlignments
(boolean storeAlignments) void
Show usage and exitMethods 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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Field Details
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onlyOneError
public static boolean onlyOneError -
MAX_ERROR_RATE
public static double MAX_ERROR_RATE -
MAX_ALIGN_LENGTH
public static int MAX_ALIGN_LENGTH
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Constructor Details
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SnpEffCmdCds
public SnpEffCmdCds() -
SnpEffCmdCds
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SnpEffCmdCds
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Method Details
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parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
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run
public boolean run()Run command- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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setCheckNumOk
public void setCheckNumOk(boolean checkNumOk) -
setMaxErrorRate
public void setMaxErrorRate(double maxErrorRate) -
setStoreAlignments
public void setStoreAlignments(boolean storeAlignments) -
usage
Show usage and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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