Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdCds
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdCds
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdCds extends SnpEff
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
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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
Fields Modifier and Type Field Description static int
MAX_ALIGN_LENGTH
static double
maxErrorPercentage
static boolean
onlyOneError
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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 SnpEffCmdCds()
SnpEffCmdCds(java.lang.String genomeVer, java.lang.String configFile, java.lang.String cdsFile)
SnpEffCmdCds(Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run commandvoid
setCheckNumOk(boolean checkNumOk)
void
setStoreAlignments(boolean storeAlignments)
void
usage(java.lang.String message)
Show usage and exit-
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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Constructor Detail
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SnpEffCmdCds
public SnpEffCmdCds()
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SnpEffCmdCds
public SnpEffCmdCds(Config config)
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SnpEffCmdCds
public SnpEffCmdCds(java.lang.String genomeVer, java.lang.String configFile, java.lang.String cdsFile)
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Method Detail
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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()
Run command- 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 and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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