public SRAFileReader(final SRAAccession acc) { this.acc = acc; if (!acc.isValid()) { throw new IllegalArgumentException("SRAFileReader: cannot resolve SRA accession '" + acc + "'\n" + "Possible causes are an invalid SRA accession or a connection problem."); } try { run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc.toString()); virtualHeader = loadSamHeader(); } catch (final Exception e) { throw new RuntimeException(e); } cachedReferences = new ReferenceCache(run, virtualHeader); recordRangeInfo = SRAIterator.getRecordsRangeInfo(run); index = new SRAIndex(virtualHeader, recordRangeInfo); }
public SRAFileReader(final SRAAccession acc) { this.acc = acc; if (!acc.isValid()) { throw new IllegalArgumentException("SRAFileReader: cannot resolve SRA accession '" + acc + "'\n" + "Possible causes are an invalid SRA accession or a connection problem."); } try { run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc.toString()); virtualHeader = loadSamHeader(); } catch (final Exception e) { throw new RuntimeException(e); } cachedReferences = new ReferenceCache(run, virtualHeader); recordRangeInfo = SRAIterator.getRecordsRangeInfo(run); index = new SRAIndex(virtualHeader, recordRangeInfo); }