Examples of calcualteAlignmentEnd()

Examples of net.sf.cram.CramRecord.calcualteAlignmentEnd()

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            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",
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Examples of net.sf.cram.CramRecord.calcualteAlignmentEnd()

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        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(),
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Examples of net.sf.cram.CramRecord.calcualteAlignmentEnd()

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          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()));

      }
    }
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Examples of net.sf.cram.CramRecord.calcualteAlignmentEnd()

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    }

    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(),
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Examples of net.sf.cram.CramRecord.calcualteAlignmentEnd()

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      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()));
  }

  @Test
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