Package org.snpsift.hwe
Class SnpSiftCmdHwe
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.hwe.SnpSiftCmdHwe
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdHwe extends SnpSift
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static int
SHOW_EVERY
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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 SnpSiftCmdHwe()
SnpSiftCmdHwe(java.lang.String[] args)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>
headers()
Headers to addstatic void
main(java.lang.String[] args)
Mainvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Analyze the file (run multi-thread mode)void
usage(java.lang.String errMsg)
Show usage and exit-
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 Detail
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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Method Detail
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main
public static void main(java.lang.String[] args)
Main
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headers
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
Description copied from class:SnpSift
Headers to add
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments
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run
public boolean run()
Analyze the file (run multi-thread mode)
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