private NsiReader(GenomeAssembly assembly, IDataSourceVersion version, string jsonKey, ReportFor reportFor, IntervalArray <string>[] intervalArrays) { Assembly = assembly; Version = version; JsonKey = jsonKey; ReportFor = reportFor; _intervalForest = new IntervalForest <string>(intervalArrays); }
public IntervalForestTests() { var intervalArraysByRefIndex = new IntervalArray <string> [3]; intervalArraysByRefIndex[0] = GetIntervalArrayRefIndex0(); intervalArraysByRefIndex[1] = GetIntervalArrayRefIndex1(); intervalArraysByRefIndex[2] = GetIntervalArrayRefIndex2(); _intervalForest = new IntervalForest <string>(intervalArraysByRefIndex); }
public SpliceAiParser(Stream stream, ISequenceProvider sequenceProvider, Dictionary <ushort, IntervalArray <byte> > spliceIntervals, IntervalForest <string> geneTree = null, Dictionary <string, List <string> > geneSynonyms = null) { _stream = stream; _sequenceProvider = sequenceProvider; _spliceIntervals = spliceIntervals; _geneTree = geneTree; _geneSynonyms = geneSynonyms; _unresolvedSymbols = new HashSet <string>(); _currentPositionGeneSymbols = new HashSet <string>(); }
public TranscriptCache(IEnumerable <IDataSourceVersion> dataSourceVersions, GenomeAssembly genomeAssembly, IntervalArray <ITranscript>[] transcriptIntervalArrays, IntervalArray <IRegulatoryRegion>[] regulatoryRegionIntervalArrays) { Name = "Transcript annotation provider"; DataSourceVersions = dataSourceVersions; Assembly = genomeAssembly; TranscriptIntervalForest = new IntervalForest <ITranscript>(transcriptIntervalArrays); RegulatoryIntervalForest = new IntervalForest <IRegulatoryRegion>(regulatoryRegionIntervalArrays); }
public MatcherTests() { var repeatNumbers = new[] { 7, 8, 9 }; double[] percentiles = { 0, 1, 1.5 }; var classificationRanges = new[] { new Interval(0, 27) }; var classifications = new[] { "Normal" }; var aInterval = new ChromosomeInterval(ChromosomeUtilities.Chr1, 100, 200); var aPhenotype = new RepeatExpansionPhenotype(aInterval, "A", null, repeatNumbers, percentiles, classifications, classificationRanges); var chr1Phenotypes = new Interval <RepeatExpansionPhenotype> [1]; chr1Phenotypes[0] = new Interval <RepeatExpansionPhenotype>(aInterval.Start, aInterval.End, aPhenotype); var intervalArrays = new IntervalArray <RepeatExpansionPhenotype> [1]; intervalArrays[ChromosomeUtilities.Chr1.Index] = new IntervalArray <RepeatExpansionPhenotype>(chr1Phenotypes); var phenotypeForest = new IntervalForest <RepeatExpansionPhenotype>(intervalArrays); _matcher = new Matcher(phenotypeForest); }
public static IEnumerable <AnnotationRange> GenerateAnnotationRanges(List <long> blockBasedOffsets, string vcfUrl, IntervalForest <IGene> geneIntervalForest, IDictionary <string, IChromosome> refNameToChromosome) { // There may be less intervals for annotation Lambda after the adjustment AnnotationPosition[] adjustedStarts = AdjustPartitionGenomicStarts(blockBasedOffsets, vcfUrl, geneIntervalForest, refNameToChromosome); return(GetRanges(adjustedStarts)); }