updateTracks(samRecords, tracks); ref = getRefBasesOfFail(cramContext, refId); sam2CramRecordFactory.setRefBases(ref); setMateInfo(cramRecords); } else { for (final CramCompressionRecord cramRecord : cramRecords) { assertSame(cramContext.samFileHeader, samRecords, cramRecords); continue; default: slice.setRefMD5(getRefBasesOfFail(cramContext, slice.sequenceId)); break;
@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); } }
CramCompressionRecord prev = mate; if (prev.next != null || prev.previous != null) { detach(r); detach(prev); continue; detach(r); detach(r); detach(r); || (last.isMateNegativeStrand() != r.isNegativeStrand()) || (r.mateAlignmentStart != last.alignmentStart) || (last.mateAlignmentStart != r.alignmentStart)) { detach(r);
Container container = CramSerilization.convert(samRecords, context); container.offset = offset; offset += ContainerIO.writeContainer(cramVersion, container, outputStream);
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); }
container = CramSerilization.convert(records, header.getSamFileHeader(), referenceSource, lossyOptions); } catch (IllegalArgumentException | IllegalAccessException | IOException e) { throw new RuntimeException(e);
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); }