Package org.snpsift
Class SnpSiftCmdAnnotate
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdAnnotate
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Annotate a VCF file with ID from another VCF file (database)
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected AnnotateVcfDb
protected boolean
protected String
protected int
protected String
protected int
protected org.snpsift.SnpSiftCmdAnnotate.AnnotationMethod
protected String
static final int
protected boolean
protected boolean
protected boolean
protected org.snpeff.fileIterator.VcfFileIterator
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 TypeMethodDescriptionboolean
annotate
(org.snpeff.vcf.VcfEntry vcfEntry) boolean
annotateInit
(org.snpeff.fileIterator.VcfFileIterator vcfFile) Initialize database for annotation processprotected List
<org.snpeff.vcf.VcfHeaderEntry> headers()
Build headers to addvoid
init()
Initialize default valuesvoid
Parse command line argumentsboolean
run()
Annotate each entry of a VCF fileList
<org.snpeff.vcf.VcfEntry> run
(boolean createList) Run annotationsvoid
setAnnotateEmpty
(boolean annotateEmpty) void
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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Field Details
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SHOW
public static final int SHOW- See Also:
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annotateEmpty
protected boolean annotateEmpty -
useId
protected boolean useId -
useInfoField
protected boolean useInfoField -
useRefAlt
protected boolean useRefAlt -
method
protected org.snpsift.SnpSiftCmdAnnotate.AnnotationMethod method -
countBadRef
protected int countBadRef -
maxBlockSize
protected int maxBlockSize -
chrPrev
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prependInfoFieldName
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existsInfoField
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infoFields
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vcfFile
protected org.snpeff.fileIterator.VcfFileIterator vcfFile -
annotateDb
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Constructor Details
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SnpSiftCmdAnnotate
public SnpSiftCmdAnnotate() -
SnpSiftCmdAnnotate
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Method Details
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) -
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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headers
Build headers to add -
init
public void init()Initialize default values -
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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setAnnotateEmpty
public void setAnnotateEmpty(boolean annotateEmpty) -
usage
Show usage message
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