Package org.snpsift
Class SnpSiftCmdExtractFields
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdExtractFields
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Extract fields from VCF file to a TXT (tab separated) format
- 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, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, 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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Constructor Details
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SnpSiftCmdExtractFields
public SnpSiftCmdExtractFields() -
SnpSiftCmdExtractFields
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Method Details
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init
public void init()Description copied from class:SnpSift
Initialize default values -
parseArgs
Parse command line arguments -
run
public boolean run()Run main algorithm -
run
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usage
Show usage message
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