Package org.snpsift
Class SnpSiftCmdVarType
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdVarType
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Annotate a VCF file with variant type
- Author:
- pablocingolani
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Field Summary
FieldsFields inherited from class org.snpsift.SnpSift
args, BUILD, command, config, configFile, dataDir, dbFileName, dbTabix, dbType, debug, download, EMPTY_ARGS, errCount, genomeVersion, help, log, needsConfig, needsDb, needsGenome, numWorkers, output, quiet, REVISION, saveOutput, shiftArgs, SHOW_EVERY_VCFLINES, showVcfHeader, showVersion, SOFTWARE_NAME, suppressOutput, vcfHeaderAddProgramVersion, vcfHeaderProcessed, vcfInputFile, verbose, VERSION, VERSION_MAJOR, VERSION_NO_NAME, VERSION_SHORT
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class org.snpsift.SnpSift
addHeaders, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, init, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb
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Field Details
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SHOW
public static final int SHOW- See Also:
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SHOW_LINES
public static final int SHOW_LINES- See Also:
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VARTYPE
- See Also:
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Constructor Details
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SnpSiftCmdVarType
public SnpSiftCmdVarType() -
SnpSiftCmdVarType
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Method Details
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) Annotate one entry -
headers
Description copied from class:SnpSift
Headers to add -
parseArgs
Parse command line arguments -
run
public boolean run()Annotate entries -
usage
Show usage message
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