SnpSiftCmdAlleleMatrix (SnpSift 5.1 API)

java.lang.Object
- org.snpsift.SnpSift
- - org.snpsift.SnpSiftCmdAlleleMatrix

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

Field Summary

Fields
Modifier and Type Field Description

static java.lang.String SEPARATOR

static int SHOW_EVERY
- 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

Constructor Summary

Constructors
Constructor Description

SnpSiftCmdAlleleMatrix()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`parseArgs(java.lang.String[] args)`	Parse command line arguments
`int`	`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 file
`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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - SEPARATOR
```
public static java.lang.String SEPARATOR
```
  - SHOW_EVERY
```
public static int SHOW_EVERY
```
- Constructor Detail
  - SnpSiftCmdAlleleMatrix
```
public SnpSiftCmdAlleleMatrix()
```
- Method Detail
  - parseArgs
```
public void parseArgs(java.lang.String[] args)
```
    Parse command line arguments
    
    Specified by:
    
    parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    parseArgs in class SnpSift
  - processStr
```
public int processStr(org.snpeff.vcf.VcfEntry vcfEntry,
                      java.lang.StringBuilder sbcodes)
```
    Process a VCF entry and return a string (tab separated values)
  - run
```
public boolean run()
```
    Process the whole VCF file
    
    Specified by:
    
    run in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    run in class SnpSift
  - usage
```
public void usage(java.lang.String msg)
```
    Show usage message
    
    Specified by:
    
    usage in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    usage in class SnpSift