Пример #1
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 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);
 }
Пример #2
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        public IntervalForestTests()
        {
            var intervalArraysByRefIndex = new IntervalArray <string> [3];

            intervalArraysByRefIndex[0] = GetIntervalArrayRefIndex0();
            intervalArraysByRefIndex[1] = GetIntervalArrayRefIndex1();
            intervalArraysByRefIndex[2] = GetIntervalArrayRefIndex2();
            _intervalForest             = new IntervalForest <string>(intervalArraysByRefIndex);
        }
Пример #3
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 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>();
 }
Пример #4
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 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);
 }
Пример #5
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        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);
        }
Пример #6
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        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));
        }