Examples of net.sf.cram.CramRecord

      for (int i = 0; i < container.slices.length; i++) {
        Slice s = container.slices[i];
        List<CramRecord> list = BLOCK_PROTO.getRecords(s, container.h,
            cramHeader.samFileHeader, new TreeMap<String, Long>());


        CramRecord first = list.get(0);
        CramRecord last = list.get(list.size() - 1);
        assertEquals(s.alignmentStart, first.getAlignmentStart());
        int end = last.calcualteAlignmentEnd();
        System.out.println(end);
        if (s.alignmentSpan != last.calcualteAlignmentEnd()
            - first.getAlignmentStart())
          fail(String
              .format("Slice %d alignment span mismatch: %d, %d, %d, %d, %d, %s, %s\n",
                  i, s.alignmentStart, s.alignmentSpan,
                  first.getAlignmentStart(),
                  last.getAlignmentStart(),
                  last.calcualteAlignmentEnd(),
                  first.getReadName(), last.getReadName()));


      }
    }


    CramRecord firstRecord1 = records.get(0);
    CramRecord lastRecord1 = records.get(records.size() - 1);
    assertEquals(container.alignmentStart, firstRecord1.getAlignmentStart());
    if (container.alignmentSpan != lastRecord1.calcualteAlignmentEnd()
        - firstRecord1.getAlignmentStart())
      fail(String
          .format("Container alignment span mismatch: %d, %d, %d, %d, %d, %s, %s\n",
              container.alignmentStart, container.alignmentSpan,
              firstRecord1.getAlignmentStart(),
              lastRecord1.getAlignmentStart(),
              lastRecord1.calcualteAlignmentEnd(),
              firstRecord1.getReadName(),
              lastRecord1.getReadName()));
  }

    assertEquals(container.nofRecords, container3.nofRecords);
    assertEquals(container.sequenceId, container3.sequenceId);


    assertEquals(records.size(), records3.size());
    for (int i = 0; i < records.size(); i++) {
      CramRecord r1 = records.get(i);
      CramRecord r3 = records3.get(i);


      assertTrue(
          "Mismatch at " + i + ":\n" + r1.toString() + "\n"
              + r3.toString(), compare(r1, r3));
    }
    
    FileOutputStream fos = new FileOutputStream(new File("./src/test/resources/data/set1/small.cram2")) ;
    fos.write(baos.getBuffer(), 0, baos.size()) ;
    fos.close() ;

Examples of net.sf.cram.CramRecord

Related Classes of net.sf.cram.CramRecord