WARNING: This is a broken commit. Everything builds with the Python C API or with Cython, but not everything tests out.
Merge branch 'merge_cython' into mt-reader

Conflicts:
	lib/parsers.cc
	lib/parsers.hh
	python/Makefile
	python/setup.py.in
Rename _khmermodule.cc.orig back to _khmermodule.cc.
added split-pe
Hack support for Config interface into Cython.
NOTE: The 'get_config' method is not quite right, due to the way Cython handles C++ references.
Comment out test corresponding to 'collect_high_abundance_kmers', which is disabled in Cython interface.
Undo breakage caused by importing 'new_counting_hash' as 'new_hashtable' in Cython merge.
Clean up directories from tests which abort abnormally.
changed assembly pipeline
added files
added membound.py
Handle differences between CPython API and Cython interfaces with a crude try-except hack during imports.
Merge branch 'master' into mt-reader
Merge branch 'qp_refactor' into mt-reader
NOTE: The 'test_count_overlap_cpp' test may be broken. Rest of commit should be good though.

Conflicts:
	lib/hashbits.cc
	lib/hashbits.hh
	tests/test_scripts.py
useful misc scripts
multi-rename script
put implicit cutoff in rename script
modify test_scripts.py, remove other code
updated
changed reporting period
disabled tests broken by my reporting change