Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdDatabases

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 org.snpeff.SnpEff

SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	DARK_ROW
static java.lang.String	FTP_PROTOCOL
static java.lang.String	HTTP_PROTOCOL
static java.lang.String	LIGHT_ROW

Fields inherited from class org.snpeff.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, 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(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run according to command line options
void	usage(java.lang.String message)	Show 'usage' message and exit with an error code '-1'

Methods inherited from class org.snpeff.SnpEff

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DARK_ROW

public static final java.lang.String DARK_ROW

See Also:

Constant Field Values

LIGHT_ROW

public static final java.lang.String LIGHT_ROW

See Also:

Constant Field Values

HTTP_PROTOCOL

public static final java.lang.String HTTP_PROTOCOL

See Also:

Constant Field Values

FTP_PROTOCOL

public static final java.lang.String FTP_PROTOCOL

See Also:

Constant Field Values

Constructor Detail

SnpEffCmdDatabases

public SnpEffCmdDatabases()

Method Detail

parseArgs

public void parseArgs(java.lang.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(java.lang.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