Package org.snpeff.spliceSites
Class SnpEffCmdSpliceAnalysis
java.lang.Object
org.snpeff.SnpEff
org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
- All Implemented Interfaces:
CommandLine
Analyze sequences from splice sites
- Author:
- pcingola
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Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic int
static int
static double
static int
static int
static final double
static final int
static final double
static final double
static final double
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, tags, tagsNo, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class org.snpeff.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, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb
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Field Details
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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:
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THRESHOLD_COUNT
public static final int THRESHOLD_COUNT- See Also:
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THRESHOLD_P
public static final double THRESHOLD_P- See Also:
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THRESHOLD_BRANCH_U12_PERCENTILE
public static final double THRESHOLD_BRANCH_U12_PERCENTILE- See Also:
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THRESHOLD_U12_OBSERVED_EXPECTED
public static final double THRESHOLD_U12_OBSERVED_EXPECTED- See Also:
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HTML_WIDTH
public static int HTML_WIDTH -
HTML_HEIGHT
public static int HTML_HEIGHT
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Constructor Details
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SnpEffCmdSpliceAnalysis
public SnpEffCmdSpliceAnalysis()
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Method Details
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parseArgs
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
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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