Begin adding support for reads containing indels, and soft-clipped and hard-clipped positions
Fix major indentation bugs in extract_and_update_methylation_index_from_single_end_read and extract_and_update_methylation_index_from_paired_end_reads.
Added sanity check to get_read_positions.
Began re-writing tests for get_read_positions. Specifically, simplify test reads and test the full range of indels and clipping.
Unit tests for get_read_positions complete.
Wrote skeleton for process_overlap function. Began associated deprecations.
Working way through logic of possible overlap_check.
Renamed get_read_positions to get_positions, to better reflect what it does.
Completed version of process_overlap; ready for testing.
Updated comethylation to use process_overlap function.
Minor style fixes.
Tests written for process_overlap.
Tests of deprecated functions removed.
Miscellaneous code tidying.
Fix broken tests.
Add test for corner case overlap.
Massive simplification to extract_and_update_methylation_index_from_single_end_reads and extract_and_update_methylation_index_from_paired_end_reads by using iterators.
Fix how m-tuples are created.
Remove None before computing min/max when computing overlap.
Don’t do arithmetic on Nones.
Don’t do arithmetic on Nones.
Merge branch 'indel_support' of https://github.com/PeteHaitch/comethylation into indel_support

Conflicts:
	comethylation/funcs.py
Include Python 3.4 in Travis-CI builds.
Update examples to use Bismark v0.12.5.