Package org.snpsift
Class SnpSiftCmdGwasCatalog
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdGwasCatalog
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- 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
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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
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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 SnpSiftCmdGwasCatalog()
SnpSiftCmdGwasCatalog(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)
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 addvoid
init()
Initialize default valuesvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsvoid
readDb()
Read databaseboolean
run()
Annotate entriesjava.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
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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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GWAS_CATALOG
public final java.lang.String GWAS_CATALOG
- See Also:
- Constant Field Values
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CONFIG_GWAS_DB_NAME
public final java.lang.String CONFIG_GWAS_DB_NAME
- See Also:
- Constant Field Values
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Method Detail
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
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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
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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readDb
public void readDb()
Read database
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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 saveResults)
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