Package org.snpsift
Class SnpSiftCmdPrivate
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdPrivate
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdPrivate extends SnpSift
Annotate if a variant is 'private'. I.e. only represented within a family (or group)- Author:
- pcingola
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Field Summary
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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 SnpSiftCmdPrivate()
SnpSiftCmdPrivate(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 ve)
Parse a single VCF entryboolean
annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run annotationsjava.util.List<org.snpeff.vcf.VcfEntry>
run(boolean createList)
Run annotations.void
usage(java.lang.String msg)
Show usage message-
Methods 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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Method Detail
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry ve)
Parse a single VCF entry
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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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parseArgs
public void parseArgs(java.lang.String[] args)
Description copied from class:SnpSift
Parse command line arguments
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run
public boolean run()
Run annotations
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run
public java.util.List<org.snpeff.vcf.VcfEntry> run(boolean createList)
Run annotations. Create a list of VcfEntries if 'createList' is true (use for test cases)
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