Package org.snpsift
Class SnpSiftCmdAnnotateMem
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdAnnotateMem
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Annotate a VCF file from another VCF file (database)
The database file is loaded into memory.
- Author:
- pcingola
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Field Summary
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add a database fileboolean
annotate
(org.snpeff.vcf.VcfEntry vcfEntry) boolean
boolean
annotateInit
(org.snpeff.fileIterator.VcfFileIterator vcfFile) Initialize database for annotation processvoid
create()
Create all databasesprotected List
<org.snpeff.vcf.VcfHeaderEntry> headers()
Build headers to addvoid
init()
Initializevoid
Parse command line argumentsboolean
run()
Annotate each entry of a VCF fileList
<org.snpeff.vcf.VcfEntry> run
(boolean createList) Run annotationsvoid
Show usage messageMethods inherited from class org.snpsift.SnpSift
addHeaders, annotateFinish, 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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Constructor Details
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SnpSiftCmdAnnotateMem
public SnpSiftCmdAnnotateMem() -
SnpSiftCmdAnnotateMem
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Method Details
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add
Add a database file -
annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) -
annotateFinish
public boolean annotateFinish() -
annotateInit
public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile) Initialize database for annotation process- Specified by:
annotateInit
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateInit
in classSnpSift
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create
public void create()Create all databases -
headers
Build headers to add -
init
public void init()Initialize -
parseArgs
Parse command line arguments -
run
public boolean run()Annotate each entry of a VCF file -
run
Run annotations- Parameters:
createList
- : If true, return a list with all annotated entries (used for test cases invalid input: '&' debugging)
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usage
Show usage message
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