Examples of net.sf.samtools.SAMSequenceRecord

net.sf.samtools.SAMSequenceRecord

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


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


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


            bis.close();


            SAMIterator it = new SAMIterator(is, refFile);

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      int candidateIndex = getIndexOfMinAlignment();
      if (candidateIndex < 0) {
        next = null;
      } else {
        next = records[candidateIndex];
        SAMSequenceRecord sequence = header.getSequence(next
            .getReferenceName());


        next.setHeader(header);


        next.setReferenceIndex(sequence.getSequenceIndex());


        next.setReadName(sources[candidateIndex].id + delim
            + next.getReadName());


        if (next.getMateReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
          next.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
        } else {
          SAMSequenceRecord mateSequence = header.getSequence(next
              .getMateReferenceName());
          next.setMateReferenceIndex(mateSequence.getSequenceIndex());
        }


        if (sources[candidateIndex].it.hasNext())
          records[candidateIndex] = sources[candidateIndex].it.next();
        else

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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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          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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      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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  }


  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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Related Classes of net.sf.samtools.SAMSequenceRecord

net.sf.cram.BLOCK_PROTO

net.sf.cram.Cram2Bam

net.sf.cram.Merge

net.sf.cram.Merge$MergedIterator

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