Ejemplo n.º 1
0
        private static ExitCodes ProgramExecution()
        {
            string cachePath = CacheConstants.TranscriptPath(_inputPrefix);

            var(refIndexToChromosome, _, _) = SequenceHelper.GetDictionaries(_compressedReferencePath);
            var cache            = TranscriptCacheHelper.GetCache(cachePath, refIndexToChromosome);
            var geneToInternalId = InternalGenes.CreateDictionary(cache.Genes);

            using (var writer = new GffWriter(GZipUtilities.GetStreamWriter(_outputFileName)))
            {
                var creator = new GffCreator(writer, geneToInternalId);
                creator.Create(cache.TranscriptIntervalArrays);
            }

            return(ExitCodes.Success);
        }
Ejemplo n.º 2
0
        private static ExitCodes ProgramExecution()
        {
            Source transcriptSource = ParseVepCacheDirectoryMain.GetSource(_transcriptSource);
            string cachePath        = CacheConstants.TranscriptPath(_inputPrefix);

            IDictionary <ushort, IChromosome> refIndexToChromosome =
                SequenceHelper.GetDictionaries(_compressedReferencePath).refIndexToChromosome;

            TranscriptCacheData      cache            = TranscriptCacheHelper.GetCache(cachePath, refIndexToChromosome);
            IDictionary <IGene, int> geneToInternalId = InternalGenes.CreateDictionary(cache.Genes);

            using (var writer = new GffWriter(GZipUtilities.GetStreamWriter(_outputFileName)))
            {
                var creator = new GffCreator(writer, geneToInternalId, transcriptSource);
                creator.Create(cache.TranscriptIntervalArrays);
            }

            return(ExitCodes.Success);
        }