private ReadCollection getReadCollection() { if (run != null) { return run; } log.debug("Recovering SRA read collection. Accession: " + accession); try { return run = NGS.openReadCollection(accession.toString()); } catch (ErrorMsg e) { throw new RuntimeException(e); } }
private ReadCollection getReadCollection() { if (run != null) { return run; } log.debug("Recovering SRA read collection. Accession: " + accession); try { return run = NGS.openReadCollection(accession.toString()); } catch (ErrorMsg e) { throw new RuntimeException(e); } }
/** * @param acc accession */ public SRAIndexedSequenceFile(SRAAccession acc) { this.acc = acc; if (!acc.isValid()) { throw new RuntimeException("Passed an invalid SRA accession into SRA reader: " + acc); } try { run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc.toString()); sequenceDictionary = loadSequenceDictionary(); } catch (final ErrorMsg e) { throw new RuntimeException(e); } reset(); }
/** * @param acc accession */ public SRAIndexedSequenceFile(SRAAccession acc) { this.acc = acc; if (!acc.isValid()) { throw new RuntimeException("Passed an invalid SRA accession into SRA reader: " + acc); } try { run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc.toString()); sequenceDictionary = loadSequenceDictionary(); } catch (final ErrorMsg e) { throw new RuntimeException(e); } reset(); }
@Override public String toString() { final String childToString; switch (type()) { case FILE: childToString = asFile().toString(); break; case PATH: childToString = asPath().toString(); break; case INPUT_STREAM: childToString = asUnbufferedInputStream().toString(); break; case SEEKABLE_STREAM: childToString = asUnbufferedSeekableStream().toString(); break; case URL: childToString = asUrl().toString(); break; case SRA_ACCESSION: childToString = asSRAAccession().toString(); break; default: throw new IllegalStateException(); } return String.format("%s:%s", type(), childToString); } }
@Override public String toString() { final String childToString; switch (type()) { case FILE: childToString = asFile().toString(); break; case PATH: childToString = asPath().toString(); break; case INPUT_STREAM: childToString = asUnbufferedInputStream().toString(); break; case SEEKABLE_STREAM: childToString = asUnbufferedSeekableStream().toString(); break; case URL: childToString = asUrl().toString(); break; case SRA_ACCESSION: childToString = asSRAAccession().toString(); break; default: throw new IllegalStateException(); } return String.format("%s:%s", type(), childToString); } }
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); }