Bwa wrapper

[saketkc]

Made a wrapper for BWA(http://bio-bwa.sourceforge.net). Added few unittests. Also the Bio.Applications call method, has been now modified to allow file writes by passing an argument to stdout/stderr as a file location.

[peterjc]

Progress report - I've made a similar but more general change to the call method on the main branch,
c4a5796

I will take care of merging your work on top of this (so you don't need to worry about updating this branch) when I can find a suitable moment.

[peterjc]

OK, that's been applied to the master - thanks :)
ea6a55f

One catch was you also need to explicitly add the doctests to the list in run_tests.py,
d896509

Related to that writing doctests for command line wrappers is tricky, see:
4351be5

Also the class docstrings were repeating all the property docstrings, so it was redundant:
6c37fe7

Finally I think the unit tests could be improved a little - there are some handle leaks, see this discussion:
http://lists.open-bio.org/pipermail/biopython-dev/2013-April/010521.html

But anyway - your first major contribution to Biopython will be in the next release, thank you :)
6712d17

[peterjc]

I fixed the handle leak in this commit, where the main aim was clearer failure messages (the test was failing on some of the buildslaves):
0c6224b