New or improved features
* Support reads containing indels (closes [25](https://github.com/PeteHaitch/comethylation/issues/25) and [#45](https://github.com/PeteHaitch/comethylation/issues/45)).
* Refined process for dealing with overlapping reads (closes [15](https://github.com/PeteHaitch/comethylation/issues/15)).
* Improved documentation (closes [82](https://github.com/PeteHaitch/comethylation/issues/82) and [#84](https://github.com/PeteHaitch/comethylation/issues/84)).
* Python 3.4 support.
Minor improvements
* Added NEWS file.
Bug fixes
* Provide default `--ir1p` and `--ir2p` (closes [79](https://github.com/PeteHaitch/comethylation/issues/79)).
* Switched to *nix style line endings (\n), rather than the Windows line endings (\r\n), for the .tsv file (closes [83](https://github.com/PeteHaitch/comethylation/issues/83)).
* Switched back to samtools instead of Picard in helper_scipts/run_comethylation.sh (closes [78](https://github.com/PeteHaitch/comethylation/issues/78)).
* Updated examples to use Bismark v0.12.5.
Internal
* Simplified creation of m-tuples.
* Added `get_positions` function to get the reference positions of all bases in a read (including `None` if no reference base, such as inserted bases or soft-clipped read-positions).
* Added `process_overlap` function to process overlapping paired-end reads using the given `--overlap-check`
:(
* Running time of `v1.3` is 2-3x slower than `v1.2`. Partly because reads with indels are no longer skipped and partly because of code simplifications. Should be able to improve performance now that some internals have been simplified.