Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdAcat

java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdAcat

All Implemented Interfaces:

CommandLine

public class SnpEffCmdAcat
extends SnpEff

ACAT: Create ACAT score for T2D project Note: This is just used to compile 'ACAT' score in T2D-GENES project, not useful at all for general audience.

Author:

pcingola

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	ACAT
static double	CONSERVATION_THRESHOLD
static java.lang.String	NCACTIVITY
static java.lang.String	NCCAT
static java.lang.String	NCCONS
static java.lang.String	NCELEMENT
static java.lang.String	NCFACTOR
static java.lang.String	NCMARK
static java.lang.String	T2D_GENES

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
SnpEffCmdAcat()

Method Summary

Modifier and Type	Method	Description
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run command
void	usage(java.lang.String message)	Show usage and exit

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

ACAT

public static final java.lang.String ACAT

See Also:

Constant Field Values

NCCAT

public static final java.lang.String NCCAT

See Also:

Constant Field Values

NCACTIVITY

public static final java.lang.String NCACTIVITY

See Also:

Constant Field Values

NCMARK

public static final java.lang.String NCMARK

See Also:

Constant Field Values

NCFACTOR

public static final java.lang.String NCFACTOR

See Also:

Constant Field Values

NCELEMENT

public static final java.lang.String NCELEMENT

See Also:

Constant Field Values

NCCONS

public static final java.lang.String NCCONS

See Also:

Constant Field Values

T2D_GENES

public static final java.lang.String T2D_GENES

See Also:

Constant Field Values

CONSERVATION_THRESHOLD

public static final double CONSERVATION_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

SnpEffCmdAcat

public SnpEffCmdAcat()

Method Detail

parseArgs

public void parseArgs(java.lang.String[] args)

Parse command line arguments

Specified by:

parseArgs in interface CommandLine

Overrides:

parseArgs in class SnpEff

run

public boolean run()

Run command

Specified by:

run in interface CommandLine

Overrides:

run in class SnpEff

usage

public void usage(java.lang.String message)

Show usage and exit

Specified by:

usage in interface CommandLine

Overrides:

usage in class SnpEff