Package org.snpsift
Class SnpSiftCmdGeneSets
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdGeneSets
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdGeneSets extends SnpSift
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
INFO_GENE_SETS
static int
SHOW
static int
SHOW_LINES
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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 SnpSiftCmdGeneSets()
SnpSiftCmdGeneSets(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 entryboolean
annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>
headers()
Headers to addvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Annotate entriesjava.util.List<org.snpeff.vcf.VcfEntry>
run(boolean createList)
void
setMsigdb(java.lang.String msigdb)
void
usage(java.lang.String msg)
Show usage message-
Methods inherited from class org.snpsift.SnpSift
addHeaders, annotateFinish, 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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INFO_GENE_SETS
public static final java.lang.String INFO_GENE_SETS
- 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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annotateInit
public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
- Specified by:
annotateInit
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateInit
in classSnpSift
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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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run
public java.util.List<org.snpeff.vcf.VcfEntry> run(boolean createList)
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setMsigdb
public void setMsigdb(java.lang.String msigdb)
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