Package org.snpsift

Class SnpSiftCmdGwasCatalog

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdGwasCatalog

All Implemented Interfaces:

org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdGwasCatalog
extends SnpSift

Annotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
java.lang.String	CONFIG_GWAS_DB_NAME
java.lang.String	GWAS_CATALOG
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
SnpSiftCmdGwasCatalog()
SnpSiftCmdGwasCatalog(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
boolean	annotate(org.snpeff.vcf.VcfEntry vcfEntry)
boolean	annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile)
boolean	annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>	headers()	Headers to add
void	init()	Initialize default values
void	parseArgs(java.lang.String[] args)	Parse command line arguments
void	readDb()	Read database
boolean	run()	Annotate entries
java.util.List<org.snpeff.vcf.VcfEntry>	run(boolean saveResults)
void	usage(java.lang.String msg)	Show usage message

Methods inherited from class org.snpsift.SnpSift

addHeaders, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, 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

GWAS_CATALOG

public final java.lang.String GWAS_CATALOG

See Also:

Constant Field Values

CONFIG_GWAS_DB_NAME

public final java.lang.String CONFIG_GWAS_DB_NAME

See Also:

Constant Field Values

Constructor Detail

SnpSiftCmdGwasCatalog

public SnpSiftCmdGwasCatalog()

SnpSiftCmdGwasCatalog

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

Method Detail

annotate

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

Specified by:

annotate in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotate in class SnpSift

annotateFinish

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

Specified by:

annotateFinish in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotateFinish 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

init

public void init()

Initialize default values

Overrides:

init 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

readDb

public void readDb()

Read database

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 saveResults)

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