Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdTranslocationsReport
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdTranslocationsReport extends SnpEff
Create an SVG representation of a Marker
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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 java.lang.String
DEFAULT_REPORT_HTML_FILE
static java.lang.String
REPORT_TEMPLATE
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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 SnpEffCmdTranslocationsReport()
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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 according to command line optionsvoid
setOnlyOneTranscript(boolean onlyOneTranscript)
void
setVcfFileName(java.lang.String vcfFileName)
void
usage(java.lang.String message)
Show 'usage;' message and exit with an error code '-1'-
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, setVerbose, usageDb, usageGeneric, usageGenericAndDb
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Field Detail
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REPORT_TEMPLATE
public static final java.lang.String REPORT_TEMPLATE
- See Also:
- Constant Field Values
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DEFAULT_REPORT_HTML_FILE
public static final java.lang.String DEFAULT_REPORT_HTML_FILE
- See Also:
- Constant Field Values
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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()
Description copied from class:SnpEff
Run according to command line options- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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setOnlyOneTranscript
public void setOnlyOneTranscript(boolean onlyOneTranscript)
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setVcfFileName
public void setVcfFileName(java.lang.String vcfFileName)
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usage
public void usage(java.lang.String message)
Show 'usage;' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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