Package org.snpsift
Class SnpSiftCmdIntervalsIndex
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdIntervalsIndex
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Filter variants that hit intervals
Use an indexed VCF file.
WARNIGN: File must be uncompressed
- Author:
- pablocingolani
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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
init()
Initialize default valuesvoid
Load all BED filesvoid
Parse command line argumentsboolean
run()
Load a file compare callsvoid
setInOffset
(int inOffset) void
Show usage messageMethods inherited from class org.snpsift.SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, 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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SnpSiftCmdIntervalsIndex
public SnpSiftCmdIntervalsIndex() -
SnpSiftCmdIntervalsIndex
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Method Details
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init
public void init()Description copied from class:SnpSift
Initialize default values -
loadIntervals
public void loadIntervals()Load all BED files- Parameters:
bedFileNames
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parseArgs
Parse command line arguments -
run
public boolean run()Load a file compare calls -
setInOffset
public void setInOffset(int inOffset) -
usage
Show usage message
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