- The ``-n``, ``-nms``, and ``-scores`` options are deprecated in favor of the new, substantially more flexible, ``-c`` and ``-o`` options. See the `docs <http://bedtools.readthedocs.org/en/latest/content/tools/merge.html>`_.
- It now supports the ``-header`` option.
- It now supports the ``-S`` option.
- The ``-n``, ``-nms``, and ``-scores`` options are deprecated in favor of the new, substantially more flexible, ``-c`` and ``-o`` options. See the `docs <http://bedtools.readthedocs.org/en/latest/content/tools/merge.html>`_.
- It now supports the ``-header`` option.
- It now supports the ``-S`` option.
2. The ``map`` tool now supports BAM input.
3. The ``jaccard`` tool is now ~3 times faster.
- It now supports the ``-split`` option.
- It now supports the ``-s`` option.
- It now supports the ``-S`` option.
- It now supports the ``-split`` option.
- It now supports the ``-s`` option.
- It now supports the ``-S`` option.
4. We have fixed several CLANG compiler issues/ Thanks to John Marshall for the thorough report.
5. We added support for "X" and "=" CIGAR operators. Thanks to Pierre Lindenbaum.