Package org.snpeff.spliceSites

Class SnpEffCmdSpliceAnalysis

java.lang.Object

org.snpeff.SnpEff

org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis

All Implemented Interfaces:

CommandLine

public class SnpEffCmdSpliceAnalysis
extends SnpEff

Analyze sequences from splice sites

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 int	HTML_HEIGHT
static int	HTML_WIDTH
static double	P_VALUE_THRESHOLD
static int	SIZE_CONSENSUS_ACCEPTOR
static int	SIZE_CONSENSUS_DONOR
static double	THRESHOLD_BRANCH_U12_PERCENTILE
static int	THRESHOLD_COUNT
static double	THRESHOLD_ENTROPY
static double	THRESHOLD_P
static double	THRESHOLD_U12_OBSERVED_EXPECTED

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
SnpEffCmdSpliceAnalysis()

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

P_VALUE_THRESHOLD

public static double P_VALUE_THRESHOLD

SIZE_CONSENSUS_DONOR

public static int SIZE_CONSENSUS_DONOR

SIZE_CONSENSUS_ACCEPTOR

public static int SIZE_CONSENSUS_ACCEPTOR

THRESHOLD_ENTROPY

public static final double THRESHOLD_ENTROPY

See Also:

Constant Field Values

THRESHOLD_COUNT

public static final int THRESHOLD_COUNT

See Also:

Constant Field Values

THRESHOLD_P

public static final double THRESHOLD_P

See Also:

Constant Field Values

THRESHOLD_BRANCH_U12_PERCENTILE

public static final double THRESHOLD_BRANCH_U12_PERCENTILE

See Also:

Constant Field Values

THRESHOLD_U12_OBSERVED_EXPECTED

public static final double THRESHOLD_U12_OBSERVED_EXPECTED

See Also:

Constant Field Values

HTML_WIDTH

public static int HTML_WIDTH

HTML_HEIGHT

public static int HTML_HEIGHT

Constructor Detail

SnpEffCmdSpliceAnalysis

public SnpEffCmdSpliceAnalysis()

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