Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdTranslocationsReport
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
- All Implemented Interfaces:
CommandLine
Create an SVG representation of a Marker
-
Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
-
Field Summary
FieldsFields 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, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Parse command line argumentsboolean
run()
Run according to command line optionsvoid
setOnlyOneTranscript
(boolean onlyOneTranscript) void
setVcfFileName
(String vcfFileName) void
Show 'usage;' message and exit with an error code '-1'Methods 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, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb
-
Field Details
-
REPORT_TEMPLATE
- See Also:
-
DEFAULT_REPORT_HTML_FILE
- See Also:
-
-
Constructor Details
-
SnpEffCmdTranslocationsReport
public SnpEffCmdTranslocationsReport()
-
-
Method Details
-
parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
-
run
public boolean run()Description copied from class:SnpEff
Run according to command line options- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
-
setOnlyOneTranscript
public void setOnlyOneTranscript(boolean onlyOneTranscript) -
setVcfFileName
-
usage
Show 'usage;' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
-