Moved from —-ignoreStart/—-ignoreEnd to the more general and useful —-ignoreCycles.
Refactored unit tests to reflect this change. 
Still need to test this on “real” data.
Moved from —-ignoreStart/—-ignoreEnd to the more general and useful —-ignoreCycles.
Refactored unit tests to reflect this change. 
Still need to test this on “real” data.
Closes #71.
Merge branch 'ignore_by_seq_cycle' of https://github.com/PeteHaitch/comethylation into ignore_by_seq_cycle
Complete redesign of command line interface to simplify it (closes #74).
Updated examples to use Bismark v0.12.2 (closes #65).
Updated READMEs to reflect changes in command line arguments.
Fixed bug in parsing multiple calls of --methylation-type.
Ran 2to3 over all source files. Installs locally on Python 2.7 and 3.4 and passes unit tests. However, examples don’t yet work on Python 3.4.
Fixed bug that meant the sum of the overlap scores was incorrect for paired-end reads aligned to the OT-strand.
Local compatibility on Python 2.7 and Python 3.4.

Will try Travis builds on Python 2.6, 2.7, 3.2, 3.3 and 3.4
Fixed .travis.yml
Verified Python 3 support in Travis-CI builds and locally (closes #75).
helper_scripts/run_comethylation.sh updated to work with new command line arguments of comethylation.
Can also now handle SAMPLE_NAME with period.
Merge branch 'ignore_by_seq_cycle' of https://github.com/PeteHaitch/comethylation into ignore_by_seq_cycle
Move creation of bytearray out of loop.
Merge pull request #77 from PeteHaitch/ignore_by_seq_cycle

Ignore by seq cycle