SnpSiftCmdFilterChrPos (SnpSift 5.1 API)

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

All Implemented Interfaces:

org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
```
public class SnpSiftCmdFilterChrPos
extends SnpSift
```
Filter using CHROM:POS only

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

SnpSiftCmdFilterChrPos()

SnpSiftCmdFilterChrPos(java.lang.String[] args)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`filter(org.snpeff.vcf.VcfEntry vcfEntry)`	Filter this line?
`void`	`parseArgs(java.lang.String[] args)`	Parse command line options
`boolean`	`run()`
`java.util.List<org.snpeff.vcf.VcfEntry>`	`run(boolean createList)`	Run filter
`void`	`usage(java.lang.String msg)`	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

- Constructor Detail
  - SnpSiftCmdFilterChrPos
```
public SnpSiftCmdFilterChrPos()
```
  - SnpSiftCmdFilterChrPos
```
public SnpSiftCmdFilterChrPos(java.lang.String[] args)
```
- Method Detail
  - filter
```
protected boolean filter(org.snpeff.vcf.VcfEntry vcfEntry)
```
    Filter this line?
    
    Returns:
    
    true if the filter is satisfied, false otherwise
  - parseArgs
```
public void parseArgs(java.lang.String[] args)
```
    Parse command line options
    
    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)
```
    Run filter
    
    Parameters:
    
    createList - : If true, create a list with the results. If false, show results on STDOUT
    
    Returns:
    
    If 'createList' is true, return a list containing all vcfEntries that passed the filter. Otherwise return null.
  - usage
```
public void usage(java.lang.String msg)
```
    Usage message
    
    Specified by:
    
    usage in interface org.snpeff.snpEffect.commandLine.CommandLine
    
    Overrides:
    
    usage in class SnpSift