SnpSiftCmdIntervals (SnpSift 5.1 API)

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

All Implemented Interfaces:

org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
```
public class SnpSiftCmdIntervals
extends SnpSift
```
Filter variants that hit intervals

Author:

pablocingolani

Field Summary
- 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

SnpSiftCmdIntervals()

SnpSiftCmdIntervals(java.lang.String[] args)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`init()`	Initialize default values
`void`	`parseArgs(java.lang.String[] args)`	Parse command line arguments
`boolean`	`run()`
`java.util.List<org.snpeff.vcf.VcfEntry>`	`run(boolean createList)`	Load a file compare calls
`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, 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

- Constructor Detail
  - SnpSiftCmdIntervals
```
public SnpSiftCmdIntervals()
```
  - SnpSiftCmdIntervals
```
public SnpSiftCmdIntervals(java.lang.String[] args)
```
- Method Detail
  - init
```
public void init()
```
    Initialize default values
    
    Overrides:
    
    init in class SnpSift
  - parseArgs
```
public void parseArgs(java.lang.String[] args)
```
    Description copied from class: SnpSift
    
    Parse command line arguments
    
    Specified by:
    
    parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    parseArgs in class SnpSift
  - run
```
public boolean run()
```
    Specified by:
    
    run in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    run in class SnpSift
  - run
```
public java.util.List<org.snpeff.vcf.VcfEntry> run(boolean createList)
```
    Load a file compare calls
    
    Parameters:
    
    fileName -
  - 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
    
    Parameters:
    
    msg -