Package org.snpsift
Class SnpSiftCmdExtractFields
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdExtractFields
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdExtractFields extends SnpSift
Extract fields from VCF file to a TXT (tab separated) format- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static int
SHOW
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Fields 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 Constructor Description SnpSiftCmdExtractFields()
SnpSiftCmdExtractFields(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
init()
Initialize default valuesvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run main algorithmjava.util.List<java.lang.String>
run(boolean createList)
void
usage(java.lang.String msg)
Show usage message-
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 Detail
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SHOW
public static final int SHOW
- See Also:
- Constant Field Values
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Method Detail
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init
public void init()
Description copied from class:SnpSift
Initialize default values
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments
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run
public boolean run()
Run main algorithm
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run
public java.util.List<java.lang.String> run(boolean createList)
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