org.snpsift.SnpSiftCmdFilterGt

All Implemented Interfaces:: org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdFilterGt extends SnpSift

Generic SnpSift genotype filter Removes genotypes matching the filter: e.g. if the expression is "GQ invalid input: '<' 20", all genotypes with quality lower than 20 will be replaced by './.' (missing)

Author:: pablocingolani

Field Summary

Fields inherited from class 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

SnpSiftCmdFilterGt()

SnpSiftCmdFilterGt(String[] args)
Method Summary

Modifier and Type

Method

Description

void

addSet(String fileName)

Read a file as a string set

List<org.snpeff.vcf.VcfEntry>

filter(String fileName, String expression, boolean createList)

Filter a file

protected List<org.snpeff.vcf.VcfHeaderEntry>

headers()

Headers to add

void

init()

Initialize default values

void

parseArgs(String[] args)

Parse command line options

Expression

parseExpression(String expression)

Parse expression

boolean

run()

List<org.snpeff.vcf.VcfEntry>

run(boolean createList)

Run filter

void

usage(String msg)

Usage message

Methods inherited from class SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, 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 Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SnpSiftCmdFilterGt
  
  public SnpSiftCmdFilterGt()
- SnpSiftCmdFilterGt
  
  public SnpSiftCmdFilterGt(String[] args)
Method Details
- addSet
  
  public void addSet(String fileName)
  
  Read a file as a string set
- filter
  
  public List<org.snpeff.vcf.VcfEntry> filter(String fileName, String expression, boolean createList)
  
  Filter a file
- headers
  
  protected List<org.snpeff.vcf.VcfHeaderEntry> headers()
  
  Description copied from class: SnpSift
  
  Headers to add
  
  Overrides:
  
  headers in class SnpSift
- init
  
  public void init()
  
  Initialize default values
  
  Overrides:
  
  init in class SnpSift
- parseArgs
  
  public void parseArgs(String[] args)
  
  Parse command line options
  
  Specified by:
  
  parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  parseArgs in class SnpSift
- parseExpression
  
  public Expression parseExpression(String expression) throws Exception
  
  Parse expression
  
  Throws:
  
  Exception
- run
  
  public boolean run()
  
  Specified by:
  
  run in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  run in class SnpSift
- run
  
  public 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(String msg)
  
  Usage message
  
  Specified by:
  
  usage in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  usage in class SnpSift

Class SnpSiftCmdFilterGt

Field Summary

Fields inherited from class SnpSift

Constructor Summary

Method Summary

Methods inherited from class SnpSift

Methods inherited from class Object

Constructor Details

SnpSiftCmdFilterGt

SnpSiftCmdFilterGt

Method Details

addSet

filter

headers

init

parseArgs

parseExpression

run

run

usage