Package org.snpsift
Class SnpSiftCmdPrivate
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdPrivate
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Annotate if a variant is 'private'. I.e. only represented within a family (or group)
- 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 TypeMethodDescriptionboolean
annotate
(org.snpeff.vcf.VcfEntry ve) Parse a single VCF entryboolean
annotateInit
(org.snpeff.fileIterator.VcfFileIterator vcfFile) void
Parse command line argumentsboolean
run()
Run annotationsList
<org.snpeff.vcf.VcfEntry> run
(boolean createList) Run annotations.void
Show usage messageMethods inherited from class org.snpsift.SnpSift
addHeaders, annotateFinish, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, 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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Constructor Details
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SnpSiftCmdPrivate
public SnpSiftCmdPrivate() -
SnpSiftCmdPrivate
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Method Details
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry ve) Parse a single VCF entry -
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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parseArgs
Description copied from class:SnpSift
Parse command line arguments -
run
public boolean run()Run annotations -
run
Run annotations. Create a list of VcfEntries if 'createList' is true (use for test cases) -
usage
Show usage message
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