Package org.snpsift
Class SnpSiftCmdVcfOperator
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdVcfOperator
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Annotate a field based on an operation (max, min, etc.) of other VCF fields
- Author:
- pcingola
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Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionprotected String
protected String[]
protected SnpSiftCmdVcfOperator.Operator
protected String
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) String[]
getArgs()
getValues
(org.snpeff.vcf.VcfEntry vcfEntry) Parse an INFO field (can be multiple valued) and return a list of Doubleprotected List
<org.snpeff.vcf.VcfHeaderEntry> headers()
Headers to addprotected double
void
Parse command line argumentsboolean
run()
AnnotateList
<org.snpeff.vcf.VcfEntry> run
(boolean createList) Run filtervoid
Show usage messageMethods inherited from class org.snpsift.SnpSift
addHeaders, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getConfig, getConfigFile, getOutput, init, 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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fields
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outField
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operator
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infoFields
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Constructor Details
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SnpSiftCmdVcfOperator
public SnpSiftCmdVcfOperator() -
SnpSiftCmdVcfOperator
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Method Details
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) -
applyOp
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getArgs
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getValues
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getValues
Parse an INFO field (can be multiple valued) and return a list of Double -
headers
Description copied from class:SnpSift
Headers to add -
initialValue
protected double initialValue() -
parseArgs
Description copied from class:SnpSift
Parse command line arguments -
run
public boolean run()Annotate -
run
Run filter- Parameters:
createList
- : If true, create a list with the results. If false, show results on STDOUT- Returns:
- If 'createList' is true, return a list containing all vcfEntries that passed the filter. Otherwise return null.
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usage
Description copied from class:SnpSift
Show usage message
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