Merge pull request #89 from PeteHaitch/indel_support

Indel support

.travis.yml

@@ -4,7 +4,7 @@ python:
   - "2.7"
   - "3.2"
   - "3.3"
-  # - "3.4" # Currently failing due to problems installing Pysam v0.7.8 in Python 3.4 see https://github.com/PeteHaitch/comethylation/issues/75
+  - "3.4"
 
 install:
     - python setup.py install

NEWS.md

@@ -0,0 +1,67 @@
+# Version 1.3.0
+
+## 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.
+
+# Version 1.2.0
+
+## New or improved features
+
+* Python 3 support (not yet Python 3.4 compatible due to limitations of current version of Pysam).
+* Include strand of m-tuple in output.
+
+## Minor improvements
+* Updated examples to use Bismark v0.12.2 (closes [#65](https://github.com/PeteHaitch/comethylation/issues/65)).
+* Update `data/run_comethylation.sh` to use command line interface introduced in `v1.1`.
+* Improved filtering of specific read-positions.
+
+## Bug fixes
+* Fixed bug that meant the sum of the overlap scores was incorrect for paired-end reads aligned to the OT-strand.
+
+## Internal
+
+# Version 1.1.0
+
+## New or improved features
+
+* Complete re-design and simplification of command line interface (closes [#74](https://github.com/PeteHaitch/comethylation/issues/74))
+* Reduced memory usage (addresses [#64](https://github.com/PeteHaitch/comethylation/issues/64)).
+* Added support for gzip and bzip2 output files (closes [#69](https://github.com/PeteHaitch/comethylation/issues/69)).
+* Added parallelisation via GNU parallel in `helper_scripts/run_comethylation.sh`(closes [#68](https://github.com/PeteHaitch/comethylation/issues/68)).
+* Ignore specific read-positions rather than just start or end (closes [#71](https://github.com/PeteHaitch/comethylation/issues/71))
+
+## Bug fixes
+* `--methylationType CHG` requires `--strandSpecific` (closes [#72](https://github.com/PeteHaitch/comethylation/issues/72)).
+
+## Internal
+
+* Refactored `WithinFragmentComethylationMTuple` class as part of memory usage improvements.
+
+# Version 1.0.0
+
+Initial public release

comethylation/__init__.py

@@ -1,4 +1,4 @@
-__version_info__ = ('1','2','0')
+__version_info__ = ('1','3','0')
 __version__ = '.'.join(__version_info__)
 
 from . import funcs