Examples of SAMSequenceRecord

Examples of net.sf.samtools.SAMSequenceRecord

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      }

      if (c.sequenceId == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
        ref = new byte[] {};
      } else if (prevSeqId < 0 || prevSeqId != c.sequenceId) {
        SAMSequenceRecord sequence = cramHeader.samFileHeader
            .getSequence(c.sequenceId);
        ReferenceSequence referenceSequence = Utils
            .trySequenceNameVariants(referenceSequenceFile,
                sequence.getSequenceName());
        ref = referenceSequence.getBases();
        {
          // hack:
          int newLines = 0;
          for (byte b : ref)
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Examples of net.sf.samtools.SAMSequenceRecord

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          fis));
      BufferedInputStream bis = new BufferedInputStream(gis);
      List<CramIndex.Entry> full = CramIndex.readIndex(gis);

      List<CramIndex.Entry> entries = new LinkedList<CramIndex.Entry>();
      SAMSequenceRecord sequence = cramHeader.samFileHeader
          .getSequence(location.sequence);
      if (sequence == null)
        throw new RuntimeException("Sequence not found: "
            + location.sequence);

      entries.addAll(CramIndex.find(full, sequence.getSequenceIndex(),
          location.start, location.end - location.start));

      bis.close();

      return entries;
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Examples of net.sf.samtools.SAMSequenceRecord

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      SAMFileHeader fileHeader, Map<String, Long> nanoMap)
      throws IllegalArgumentException, IllegalAccessException,
      IOException {
    String seqName = SAMRecord.NO_ALIGNMENT_REFERENCE_NAME;
    if (s.sequenceId != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
      SAMSequenceRecord sequence = fileHeader.getSequence(s.sequenceId);
      seqName = sequence.getSequenceName();
    }
    DataReaderFactory f = new DataReaderFactory();
    Map<Integer, InputStream> inputMap = new HashMap<Integer, InputStream>();
    for (Integer exId : s.external.keySet()) {
      inputMap.put(exId, new ByteArrayInputStream(s.external.get(exId)
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Examples of net.sf.samtools.SAMSequenceRecord

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  }

  private static void randomStressTest() throws IOException,
      IllegalArgumentException, IllegalAccessException {
    SAMFileHeader samFileHeader = new SAMFileHeader();
    SAMSequenceRecord sequenceRecord = new SAMSequenceRecord("chr1", 100);
    samFileHeader.addSequence(sequenceRecord);

    long baseCount = 0;
    Random random = new Random();
    List<CramRecord> records = new ArrayList<CramRecord>();
    for (int i = 0; i < 100000; i++) {
      int len = random.nextInt(100) + 50;
      byte[] bases = new byte[len];
      byte[] scores = new byte[len];
      for (int p = 0; p < len; p++) {
        bases[p] = "ACGT".getBytes()[random.nextInt(4)];
        scores[p] = (byte) (33 + random.nextInt(40));
      }

      CramRecord record = new CramRecord();
      record.setReadBases(bases);
      record.setQualityScores(scores);
      record.setReadLength(record.getReadBases().length);
      record.setFlags(random.nextInt(1000));
      record.alignmentStartOffsetFromPreviousRecord = random.nextInt(200);

      byte[] name = new byte[random.nextInt(5) + 5];
      for (int p = 0; p < name.length; p++)
        name[p] = (byte) (65 + random.nextInt(10));
      record.setReadName(new String(name));

      record.setSequenceName(sequenceRecord.getSequenceName());
      record.sequenceId = sequenceRecord.getSequenceIndex();
      record.setReadMapped(random.nextBoolean());
      record.resetFlags();
      record.setReadFeatures(new ArrayList<ReadFeature>());
      record.setMappingQuality((byte) random.nextInt(40));
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