Package org.snpsift
Class SnpSiftCmdGeneSets
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdGeneSets
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)
- Author:
- pablocingolani
-
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
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
annotate
(org.snpeff.vcf.VcfEntry vcfEntry) Annotate one entryboolean
annotateInit
(org.snpeff.fileIterator.VcfFileIterator vcfFile) protected List
<org.snpeff.vcf.VcfHeaderEntry> headers()
Headers to addvoid
Parse command line argumentsboolean
run()
Annotate entriesList
<org.snpeff.vcf.VcfEntry> run
(boolean createList) void
void
Show usage messageMethods 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
-
Field Details
-
SHOW
public static final int SHOW- See Also:
-
SHOW_LINES
public static final int SHOW_LINES- See Also:
-
INFO_GENE_SETS
- See Also:
-
-
Constructor Details
-
SnpSiftCmdGeneSets
public SnpSiftCmdGeneSets() -
SnpSiftCmdGeneSets
-
-
Method Details
-
annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) Annotate one entry -
annotateInit
public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile) - Specified by:
annotateInit
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateInit
in classSnpSift
-
headers
Description copied from class:SnpSift
Headers to add -
parseArgs
Parse command line arguments -
run
public boolean run()Annotate entries -
run
-
setMsigdb
-
usage
Show usage message
-