SnpSiftCmdGt (SnpSift 5.1 API)

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

All Implemented Interfaces:

org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
```
public class SnpSiftCmdGt
extends SnpSift
```
Add genotype information to INFO fields

Author:

pcingola

Field Summary

Fields
Modifier and Type Field Description

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

SnpSiftCmdGt()

SnpSiftCmdGt(java.lang.String[] args)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.String`	`getOutput()`
`protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>`	`headers()`	Headers to add
`void`	`parseArgs(java.lang.String[] args)`	Parse command line arguments
`boolean`	`run()`	Process a VCF entry and return a string (tab separated values)
`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, 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
  - SHOW_EVERY
```
public static int SHOW_EVERY
```
- Constructor Detail
  - SnpSiftCmdGt
```
public SnpSiftCmdGt()
```
  - SnpSiftCmdGt
```
public SnpSiftCmdGt(java.lang.String[] args)
```
- Method Detail
  - getOutput
```
public java.lang.String getOutput()
```
    Overrides:
    
    getOutput in class SnpSift
  - headers
```
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
```
    Description copied from class: SnpSift
    
    Headers to add
    
    Overrides:
    
    headers in class SnpSift
  - 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
  - run
```
public boolean run()
```
    Process a VCF entry and return a string (tab separated values)
    
    Specified by:
    
    run in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    run in class SnpSift
  - usage
```
public void usage(java.lang.String msg)
```
    Description copied from class: SnpSift
    
    Show usage message
    
    Specified by:
    
    usage in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    usage in class SnpSift