@Bean public JannovarData jannovarData() { logger.info("Stubbing Jannovar data"); return new JannovarData(HG19RefDictBuilder.build(), ImmutableList.of()); }
public static JannovarData toJannovarData(JannovarProto.JannovarData protoJannovarData) { logger.debug("Converting to jannovar data..."); ReferenceDictionary referenceDictionary = toReferenceDictionary(protoJannovarData.getReferenceDictionary()); ImmutableList<TranscriptModel> transcriptModels = protoJannovarData.getTranscriptModelsList() .parallelStream() .map(toTranscriptModel(referenceDictionary)) .collect(ImmutableList.toImmutableList()); logger.debug("Done"); return new JannovarData(referenceDictionary, transcriptModels); }
ImmutableList<TranscriptModel> transcripts = parseTranscripts(refDict, targetDir); return new JannovarData(refDict, transcripts);