SnpSiftCmdHwe (SnpSift 5.1 API)

java.lang.Object
- org.snpsift.SnpSift
- - org.snpsift.hwe.SnpSiftCmdHwe

All Implemented Interfaces:

org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
```
public class SnpSiftCmdHwe
extends SnpSift
```
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file

Author:

pablocingolani

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

SnpSiftCmdHwe()

SnpSiftCmdHwe(java.lang.String[] args)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>`	`headers()`	Headers to add
`static void`	`main(java.lang.String[] args)`	Main
`void`	`parseArgs(java.lang.String[] args)`	Parse command line arguments
`boolean`	`run()`	Analyze the file (run multi-thread mode)
`void`	`usage(java.lang.String errMsg)`	Show usage and exit

Methods inherited from class org.snpsift.SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, init, isOpt, loadConfig, 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 final int SHOW_EVERY
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SnpSiftCmdHwe
```
public SnpSiftCmdHwe()
```
  - SnpSiftCmdHwe
```
public SnpSiftCmdHwe(java.lang.String[] args)
```
- Method Detail
  - main
```
public static void main(java.lang.String[] args)
```
    Main
  - 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()
```
    Analyze the file (run multi-thread mode)
    
    Specified by:
    
    run in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    run in class SnpSift
  - usage
```
public void usage(java.lang.String errMsg)
```
    Show usage and exit
    
    Specified by:
    
    usage in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    usage in class SnpSift