Package org.snpsift
Class SnpSiftCmdGt
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdGt
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdGt extends SnpSift
Add genotype information to INFO fields- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static int
SHOW_EVERY
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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 SnpSiftCmdGt()
SnpSiftCmdGt(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getOutput()
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>
headers()
Headers to addvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Process a VCF entry and return a string (tab separated values)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, 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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Method Detail
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headers
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
Description copied from class:SnpSift
Headers to add
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments
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run
public boolean run()
Process a VCF entry and return a string (tab separated values)
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