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

public class SnpSiftCmdGeneSets
extends SnpSift

Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	INFO_GENE_SETS
static int	SHOW
static int	SHOW_LINES

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

Constructor Summary

Constructors

Constructor	Description
SnpSiftCmdGeneSets()
SnpSiftCmdGeneSets(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
boolean	annotate(org.snpeff.vcf.VcfEntry vcfEntry)	Annotate one entry
boolean	annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>	headers()	Headers to add
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Annotate entries
java.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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SHOW

public static final int SHOW

See Also:

Constant Field Values

SHOW_LINES

public static final int SHOW_LINES

See Also:

Constant Field Values

INFO_GENE_SETS

public static final java.lang.String INFO_GENE_SETS

See Also:

Constant Field Values

Constructor Detail

SnpSiftCmdGeneSets

public SnpSiftCmdGeneSets()

SnpSiftCmdGeneSets

public SnpSiftCmdGeneSets(java.lang.String[] args)

Method Detail

annotate

public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)

Annotate one entry

Specified by:

annotate in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotate in class SnpSift

annotateInit

public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)

Specified by:

annotateInit in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotateInit in class SnpSift

headers

protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()

Description copied from class: SnpSift

Headers to add

Overrides:

headers in class SnpSift

parseArgs

public void parseArgs(java.lang.String[] args)

Parse command line arguments

Specified by:

parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

parseArgs in class SnpSift

run

public boolean run()

Annotate entries

Specified by:

run in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

run in class SnpSift

run

public java.util.List<org.snpeff.vcf.VcfEntry> run(boolean createList)

setMsigdb

public void setMsigdb(java.lang.String msigdb)

usage

public void usage(java.lang.String msg)

Show usage message

Specified by:

usage in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

usage in class SnpSift