Package org.snpsift
Class SnpSiftCmdRemoveReferenceGenotypes
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Removes reference genotypes.
I.e. replaces the genotype string by the MISSING string ('.') if the genotype is just homozygous reference (e.g. '0/0')
- 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
ConstructorsConstructorDescription -
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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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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SnpSiftCmdRemoveReferenceGenotypes
public SnpSiftCmdRemoveReferenceGenotypes() -
SnpSiftCmdRemoveReferenceGenotypes
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Method Details
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parseArgs
Description copied from class:SnpSift
Parse command line arguments -
run
public boolean run()Analyze the file -
usage
Show usage and exit
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