Package org.snpsift
Class SnpSiftCmdTsTv
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdTsTv
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdTsTv extends SnpSift
Calculate Ts/Tv rations per sample (transitions vs transversions)- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static int
SHOW_EVERY
static int
SHOW_EVERY_NL
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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 SnpSiftCmdTsTv()
SnpSiftCmdTsTv(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
error(java.lang.Throwable e, java.lang.String message)
Show an error (if not 'quiet' mode)void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Analyze the filevoid
usage(java.lang.String errMsg)
Show usage and exit-
Methods inherited from class org.snpsift.SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, 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 Detail
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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SHOW_EVERY_NL
public static final int SHOW_EVERY_NL
- See Also:
- Constant Field Values
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