Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdClosest
- java.lang.Object
-
- org.snpeff.SnpEff
-
- org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
-
- All Implemented Interfaces:
CommandLine
public class SnpEffCmdClosest extends SnpEff
Command line: Find closes marker to each variant- Author:
- pcingola
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
-
-
Field Summary
Fields Modifier and Type Field Description static java.lang.String
CLOSEST
static java.lang.String
INFO_LINE
-
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
-
-
Constructor Summary
Constructors Constructor Description SnpEffCmdClosest()
SnpEffCmdClosest(Config config)
-
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
setVerbose(boolean verbose)
void
usage(java.lang.String message)
Show usage and exit-
Methods inherited from class org.snpeff.SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, 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, usageDb, usageGeneric, usageGenericAndDb
-
-
-
-
Field Detail
-
CLOSEST
public static final java.lang.String CLOSEST
- See Also:
- Constant Field Values
-
INFO_LINE
public static final java.lang.String INFO_LINE
- See Also:
- Constant Field Values
-
-
Constructor Detail
-
SnpEffCmdClosest
public SnpEffCmdClosest()
-
SnpEffCmdClosest
public SnpEffCmdClosest(Config config)
-
-
Method Detail
-
parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
-
run
public boolean run()
Run command- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
-
setVerbose
public void setVerbose(boolean verbose)
- Overrides:
setVerbose
in classSnpEff
-
usage
public void usage(java.lang.String message)
Show usage and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
-
-