Package org.snpsift.caseControl
Class SnpSiftCmdCaseControlSummary
java.lang.Object
org.snpsift.SnpSift
org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Summarize a VCF annotated file
- Author:
- pcingola
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Field Summary
FieldsFields 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, 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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Field Details
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formatVersion
public static org.snpeff.vcf.EffFormatVersion formatVersion -
CaseControl
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Constructor Details
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SnpSiftCmdCaseControlSummary
public SnpSiftCmdCaseControlSummary() -
SnpSiftCmdCaseControlSummary
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Method Details
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parseArgs
Description copied from class:SnpSift
Parse command line arguments -
run
public boolean run()Run summary -
usage
Show usage message
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