Package org.snpsift.hwe
Class SnpSiftCmdHwe
java.lang.Object
org.snpsift.SnpSift
org.snpsift.hwe.SnpSiftCmdHwe
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file
- Author:
- pablocingolani
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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, init, isOpt, loadConfig, 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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SHOW_EVERY
public static final int SHOW_EVERY- See Also:
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Constructor Details
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SnpSiftCmdHwe
public SnpSiftCmdHwe() -
SnpSiftCmdHwe
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Method Details
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main
Main -
headers
Description copied from class:SnpSift
Headers to add -
parseArgs
Parse command line arguments -
run
public boolean run()Analyze the file (run multi-thread mode) -
usage
Show usage and exit
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