Package org.snpeff.spliceSites
Class SnpEffCmdSpliceAnalysis
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdSpliceAnalysis extends SnpEff
Analyze sequences from splice sites- Author:
- pcingola
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Nested Class Summary
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Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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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
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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
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Constructor Summary
Constructors Constructor Description SnpEffCmdSpliceAnalysis()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run according to command line optionsvoid
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
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Field Detail
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P_VALUE_THRESHOLD
public static double P_VALUE_THRESHOLD
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SIZE_CONSENSUS_DONOR
public static int SIZE_CONSENSUS_DONOR
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SIZE_CONSENSUS_ACCEPTOR
public static int SIZE_CONSENSUS_ACCEPTOR
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THRESHOLD_ENTROPY
public static final double THRESHOLD_ENTROPY
- See Also:
- Constant Field Values
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THRESHOLD_COUNT
public static final int THRESHOLD_COUNT
- See Also:
- Constant Field Values
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THRESHOLD_P
public static final double THRESHOLD_P
- See Also:
- Constant Field Values
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THRESHOLD_BRANCH_U12_PERCENTILE
public static final double THRESHOLD_BRANCH_U12_PERCENTILE
- See Also:
- Constant Field Values
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THRESHOLD_U12_OBSERVED_EXPECTED
public static final double THRESHOLD_U12_OBSERVED_EXPECTED
- See Also:
- Constant Field Values
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HTML_WIDTH
public static int HTML_WIDTH
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HTML_HEIGHT
public static int HTML_HEIGHT
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Method Detail
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parseArgs
public void parseArgs(java.lang.String[] args)
Description copied from class:SnpEff
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
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run
public boolean run()
Description copied from class:SnpEff
Run according to command line options- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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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 interfaceCommandLine
- Overrides:
usage
in classSnpEff
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