Package org.snpsift
Class SnpSiftCmdAlleleMatrix
java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdAlleleMatrix
- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
Convert VCf file to allele matrix
Note: Only use SNPs
Note: Only variants with two possible alleles. I.e. the matrix has three possible values in each cell:
- 0, for allele 0/0
- 1, for allele 0/1 or 1/0
- 2, for allele 1/1
- Author:
- pcingola
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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
Modifier and TypeMethodDescriptionvoid
Parse command line argumentsint
processStr
(org.snpeff.vcf.VcfEntry vcfEntry, StringBuilder sbcodes) Process a VCF entry and return a string (tab separated values)boolean
run()
Process the whole VCF filevoid
Show usage messageMethods 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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SEPARATOR
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SHOW_EVERY
public static int SHOW_EVERY
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Constructor Details
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SnpSiftCmdAlleleMatrix
public SnpSiftCmdAlleleMatrix()
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Method Details
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parseArgs
Parse command line arguments -
processStr
Process a VCF entry and return a string (tab separated values) -
run
public boolean run()Process the whole VCF file -
usage
Show usage message
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