Package org.snpsift
Class SnpSiftCmdIntervalsIndex
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdIntervalsIndex
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdIntervalsIndex extends SnpSift
Filter variants that hit intervals Use an indexed VCF file. WARNIGN: File must be uncompressed- Author:
- pablocingolani
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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 SnpSiftCmdIntervalsIndex()
SnpSiftCmdIntervalsIndex(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
init()
Initialize default valuesvoid
loadIntervals()
Load all BED filesvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Load a file compare callsvoid
setInOffset(int inOffset)
void
usage(java.lang.String msg)
Show usage message-
Methods 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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Method Detail
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init
public void init()
Description copied from class:SnpSift
Initialize default values
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loadIntervals
public void loadIntervals()
Load all BED files- Parameters:
bedFileNames
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments
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run
public boolean run()
Load a file compare calls
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setInOffset
public void setInOffset(int inOffset)
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