Package org.snpsift
Class SnpSiftCmdCovarianceMatrix
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdCovarianceMatrix
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdCovarianceMatrix extends SnpSift
Convert allele 'matrix' file into Covariance matrix 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 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 SnpSiftCmdCovarianceMatrix()
SnpSiftCmdCovarianceMatrix(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
covariance()
Calculate covariance matrixvoid
mean()
Calculate meanvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Process the whole filejava.lang.String
toString()
void
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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covariance
public void covariance()
Calculate covariance matrix
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mean
public void mean()
Calculate mean
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments
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run
public boolean run()
Process the whole file
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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