work in progress
About to make the threading a little more palatable.

Integrating with GroopM and finding small bugs along the way
Made threading friendlier.
Completely removed any reference to typeBam in the python, all is parseBam now.
Updated the readme to reflect changes.
Changed to LGPL to allow use in downstream projects by non-GPL zealots
With a particular focus on the upcomming StoreM project
Removed the c/bam folder structure and moved examples into a named folder
Added functionality to write files. Unfortunately it's really quite slow.
Trying something new...
Totally broke the code trying to fix / write bamm extract. Fixed it now
Added many doc strings. Version 1 of bamm is almost complete!
No need for c-based zipping anymore
Looks like all the bugs are gone

Been PEP-8'n the code, The C is now well formatted. All but 3
python files are done.

Unit tests next and then docs.
All the code is in nice shape now.
Time for unit tests
Needed this foreszser!!
Major changes. mostly working in all respect now
Large refactoring to make different coverage calculations easier to implement.

Managed to decouple calculating links from being forced to do coverage.
Code always types bamfiles now.
first stab at implementing trimmed mean coverage
typo
Merge remote-tracking branch 'official/integrating' into integrating
trimmed mean coverage appears accessible from cmdline, other assorted changes
getting ready for bens new functions
Added in all but one of the extra coverage calculators / estimators
Now to merge Bens changes
Merge branch 'trimmed_mean_coverage' of github.com:wwood/BamM into HEAD

Made sure Ben's changes meshed correctly. Looks good now.

Conflicts:
	c/coverageEstimators.c
	c/coverageEstimators.h
	c/test.c
Merge pull request #2 from wwood/integrating

Integrating