Package org.snpsift
Class SnpSiftCmdTsTv
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdTsTv
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Calculate Ts/Tv rations per sample (transitions vs transversions)
- 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, 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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SHOW_EVERY
public static final int SHOW_EVERY- See Also:
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SHOW_EVERY_NL
public static final int SHOW_EVERY_NL- See Also:
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Constructor Details
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SnpSiftCmdTsTv
public SnpSiftCmdTsTv() -
SnpSiftCmdTsTv
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Method Details
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error
Show an error (if not 'quiet' mode) -
parseArgs
Parse command line arguments -
run
public boolean run()Analyze the file -
usage
Show usage and exit
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