1. Bug fix to intersect causing BAM footers to be erroneously written when -b is BAM
2. Speedup for the map tool.
   http://bedtools.readthedocs.org/en/latest/_images/map-speed-comparo.png
3. Map tool now allows multiple columns and operations in a single run.
   http://bedtools.readthedocs.org/en/latest/content/tools/map.html#multiple-operations-and-columns-at-the-same-time