Package org.snpsift
Class SnpSiftCmdAlleleMatrix
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdAlleleMatrix
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdAlleleMatrix extends SnpSift
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
Fields Modifier and Type Field Description static java.lang.String
SEPARATOR
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 SnpSiftCmdAlleleMatrix()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
parseArgs(java.lang.String[] args)
Parse command line argumentsint
processStr(org.snpeff.vcf.VcfEntry vcfEntry, java.lang.StringBuilder sbcodes)
Process a VCF entry and return a string (tab separated values)boolean
run()
Process the whole VCF filevoid
usage(java.lang.String msg)
Show usage message-
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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Method Detail
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments
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processStr
public int processStr(org.snpeff.vcf.VcfEntry vcfEntry, java.lang.StringBuilder sbcodes)
Process a VCF entry and return a string (tab separated values)
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run
public boolean run()
Process the whole VCF file
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