Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdEff
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdEff
- All Implemented Interfaces:
CommandLine
,VcfAnnotator
Command line program: Predict variant effects
- Author:
- Pablo Cingolani
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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 final String
static final String
static final String
static final int
static final String
static final String
static final String
static final String
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, 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
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
addHeaders
(VcfFileIterator vcfFile) Add annotation headers to VCF fileboolean
Annotate: Calculate the effect of variants and show resultsboolean
Annotate a VCF entryboolean
annotateFinish
(VcfFileIterator vcfFile) Finish annotations and create reportsprotected void
annotateInit
(String outputFile) Calculate the effect of variants and show resultsboolean
annotateInit
(VcfFileIterator vcfFile) Initialize annotator: This method is called after vcfFile is opened, but before the header is output.int
void
Parse command line argumentsAdditional values to be reportedboolean
run()
Run according to command line optionsrun
(boolean createList) Run according to command line optionsvoid
setFormatVersion
(EffFormatVersion formatVersion) 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, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setTesting, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.snpeff.snpEffect.commandLine.CommandLine
getArgs
Methods inherited from interface org.snpeff.snpEffect.VcfAnnotator
setConfig, setDebug, setVerbose
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Field Details
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TEMPLATES_DIR
- See Also:
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SUMMARY_TEMPLATE
- See Also:
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SUMMARY_CSV_TEMPLATE
- See Also:
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SUMMARY_GENES_TEMPLATE
- See Also:
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DEFAULT_SUMMARY_HTML_FILE
- See Also:
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DEFAULT_SUMMARY_CSV_FILE
- See Also:
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DEFAULT_SUMMARY_GENES_FILE
- See Also:
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SHOW_EVERY
public static final int SHOW_EVERY- See Also:
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Constructor Details
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SnpEffCmdEff
public SnpEffCmdEff()
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Method Details
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addHeaders
Description copied from interface:VcfAnnotator
Add annotation headers to VCF file- Specified by:
addHeaders
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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annotate
Annotate: Calculate the effect of variants and show results -
annotate
Annotate a VCF entry- Specified by:
annotate
in interfaceVcfAnnotator
- Returns:
- true if the entry was annotated
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annotateFinish
Finish annotations and create reports- Specified by:
annotateFinish
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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annotateInit
Calculate the effect of variants and show results -
annotateInit
Description copied from interface:VcfAnnotator
Initialize annotator: This method is called after vcfFile is opened, but before the header is output. The first vcfEntry might have (and often has) already been read from the file.- Specified by:
annotateInit
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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getChangeEffectResutStats
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getTotalErrs
public int getTotalErrs() -
getvariantStats
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parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
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reportValues
Description copied from class:SnpEff
Additional values to be reported- Overrides:
reportValues
in classSnpEff
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run
public boolean run()Run according to command line options- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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run
Run according to command line options -
setFormatVersion
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usage
Show 'usage;' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
- Parameters:
message
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