public static Container convert(List<SAMRecord> samRecords, CramContext cramContext) throws IllegalArgumentException, IllegalAccessException, IOException { return convert(samRecords, cramContext, getSpans(samRecords)); }
@Override public void run() { try { container = CramSerilization.convert(records, samFileHeader, source, lossyOptions); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ContainerIO.writeContainer(cramVersion, container, baos); bytes = baos.toByteArray(); batchResultQueue.put(this); } catch (Exception e) { exceptionInWorker(e); } }
public static Container convert(List<SAMRecord> samRecords, SAMFileHeader samFileHeader, ReferenceSource source, CramLossyOptions lossyOptions) throws IllegalArgumentException, IllegalAccessException, IOException { CramContext context = new CramContext(samFileHeader, source, lossyOptions); Map<Integer, AlignmentSpan> spans = getSpans(samRecords); return convert(samRecords, context, spans); }
public static Container convertLossless(List<SAMRecord> samRecords, SAMFileHeader samFileHeader, ReferenceSource source) throws IllegalArgumentException, IllegalAccessException, IOException { CramContext context = new CramContext(samFileHeader, source, CramLossyOptions.lossless()); Map<Integer, AlignmentSpan> spans = getSpans(samRecords); return convert(samRecords, context, spans); }
Container container = CramSerilization.convert(samRecords, context); container.offset = offset; offset += ContainerIO.writeContainer(cramVersion, container, outputStream);
container = CramSerilization.convert(records, header.getSamFileHeader(), referenceSource, lossyOptions); } catch (IllegalArgumentException | IllegalAccessException | IOException e) { throw new RuntimeException(e);