java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases

All Implemented Interfaces:: CommandLine

public class SnpEffCmdDatabases extends SnpEff

Show all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menu

Author:: pablocingolani

Nested Class Summary

Nested classes/interfaces inherited from class SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
Field Summary

Fields

Modifier and Type

Field

Description

static final String

DARK_ROW

static final String

FTP_PROTOCOL

static final String

HTTP_PROTOCOL

static final String

LIGHT_ROW

Fields inherited from class SnpEff
args, BUILD, BUILD_DATE, canonical, canonicalFile, command, COMMAND_LINE_WIDTH, config, configFile, configOverride, customIntervalFiles, dataDir, debug, DEFAULT_COMMAND, download, expandIub, filterIntervalFiles, genome, genomeVer, help, hgvs, hgvsForce, hgvsOld, hgvsOneLetterAa, hgvsShift, hgvsTrId, interaction, log, maxTranscriptSupportLevel, motif, multiThreaded, nextProt, nextProtKeepAllTrs, noGenome, numWorkers, onlyProtein, onlyRegulation, onlyTranscriptsFile, output, quiet, regulationTracks, REVISION, saveOutput, shiftArgs, snpEffCmd, SOFTWARE_NAME, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, spliceSiteSize, strict, suppressOutput, tags, tagsNo, testing, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
Constructor Summary

Constructors

Constructor

Description

SnpEffCmdDatabases()
Method Summary

Modifier and Type

Method

Description

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Run according to command line options

void

usage(String message)

Show 'usage' message and exit with an error code '-1'

Methods inherited from class SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, filterTags, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, main, reportValues, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setTesting, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- DARK_ROW
  public static final String DARK_ROW
  
  See Also:
  
  Constant Field Values
- LIGHT_ROW
  public static final String LIGHT_ROW
  
  See Also:
  
  Constant Field Values
- HTTP_PROTOCOL
  public static final String HTTP_PROTOCOL
  
  See Also:
  
  Constant Field Values
- FTP_PROTOCOL
  public static final String FTP_PROTOCOL
  
  See Also:
  
  Constant Field Values
Constructor Details
- SnpEffCmdDatabases
  
  public SnpEffCmdDatabases()
Method Details
- parseArgs
  
  public void parseArgs(String[] args)
  
  Description copied from class: SnpEff
  
  Parse command line arguments
  
  Specified by:
  
  parseArgs in interface CommandLine
  
  Overrides:
  
  parseArgs in class SnpEff
- run
  
  public boolean run()
  
  Description copied from class: SnpEff
  
  Run according to command line options
  
  Specified by:
  
  run in interface CommandLine
  
  Overrides:
  
  run in class SnpEff
- usage
  
  public void usage(String message)
  
  Description copied from class: SnpEff
  
  Show 'usage' message and exit with an error code '-1'
  
  Specified by:
  
  usage in interface CommandLine
  
  Overrides:
  
  usage in class SnpEff

Class SnpEffCmdDatabases

Nested Class Summary

Nested classes/interfaces inherited from class SnpEff

Field Summary

Fields inherited from class SnpEff

Constructor Summary

Method Summary

Methods inherited from class SnpEff

Methods inherited from class Object

Field Details

DARK_ROW

LIGHT_ROW

HTTP_PROTOCOL

FTP_PROTOCOL

Constructor Details

SnpEffCmdDatabases

Method Details

parseArgs

run

usage