Package org.snpsift
Class SnpSiftCmdIntervals
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdIntervals
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Filter variants that hit intervals
- 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
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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Constructor Details
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SnpSiftCmdIntervals
public SnpSiftCmdIntervals() -
SnpSiftCmdIntervals
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Method Details
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init
public void init()Initialize default values -
parseArgs
Description copied from class:SnpSift
Parse command line arguments -
run
public boolean run() -
run
Load a file compare calls- Parameters:
fileName
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usage
Show usage message
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