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
Annotate a VCF file using GWAS catalog database
Loads GWAS catalog in memory, thus it makes no assumption about order.
- Author:
- pablocingolani
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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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
annotate
(org.snpeff.vcf.VcfEntry vcfEntry) boolean
annotateFinish
(org.snpeff.fileIterator.VcfFileIterator vcfFile) boolean
annotateInit
(org.snpeff.fileIterator.VcfFileIterator vcfFile) protected List
<org.snpeff.vcf.VcfHeaderEntry> headers()
Headers to addvoid
init()
Initialize default valuesvoid
Parse command line argumentsvoid
readDb()
Read databaseboolean
run()
Annotate entriesList
<org.snpeff.vcf.VcfEntry> run
(boolean saveResults) void
Show usage messageMethods 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
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Field Details
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SHOW
public static final int SHOW- See Also:
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SHOW_LINES
public static final int SHOW_LINES- See Also:
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GWAS_CATALOG
- See Also:
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CONFIG_GWAS_DB_NAME
- See Also:
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Constructor Details
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SnpSiftCmdGwasCatalog
public SnpSiftCmdGwasCatalog() -
SnpSiftCmdGwasCatalog
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Method Details
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) -
annotateFinish
public boolean annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile) - Specified by:
annotateFinish
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateFinish
in classSnpSift
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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
Description copied from class:SnpSift
Headers to add -
init
public void init()Initialize default values -
parseArgs
Parse command line arguments -
readDb
public void readDb()Read database -
run
public boolean run()Annotate entries -
run
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usage
Show usage message
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