Package org.snpsift
Class SnpSiftCmdVarType
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdVarType
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdVarType extends SnpSift
Annotate a VCF file with variant type- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static int
SHOW
static int
SHOW_LINES
static java.lang.String
VARTYPE
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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 SnpSiftCmdVarType()
SnpSiftCmdVarType(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
annotate(org.snpeff.vcf.VcfEntry vcfEntry)
Annotate one entryprotected java.util.List<org.snpeff.vcf.VcfHeaderEntry>
headers()
Headers to addvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Annotate entriesvoid
usage(java.lang.String msg)
Show usage message-
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 Detail
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SHOW
public static final int SHOW
- See Also:
- Constant Field Values
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SHOW_LINES
public static final int SHOW_LINES
- See Also:
- Constant Field Values
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VARTYPE
public static final java.lang.String VARTYPE
- See Also:
- Constant Field Values
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Method Detail
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
Annotate one entry
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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()
Annotate entries
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