Changelog
=========

Here you can see the full list of changes between each Wiggelen release.


Version 0.4.1
-------------

Released on May 3rd 2014.

- New ``--share-y`` and ``--y-lim`` options for ``wiggelen plot`` command.
- Command line or importable definition of custom merge function for
  ``wiggelen merge`` command.
- Optionally only report posititions in regions defined by the ``--genome``
  argument for ``wiggelen fill`` command.


Version 0.4.0
-------------

Released on February 17th 2014.

- Command line interface to `wiggelen.fill`.
- Fix off-by-one error in reading genome file argument in ``wiggelen plot``
  command.
- New merger functions `ctz` (*c*losest *t*o *z*ero), and `max` (thanks Jeroen
  F.J. Laros).


Version 0.3.0
-------------

Released on November 29th 2013.

- New merger functions `min`, `div`, and `intersect` (thanks Jeroen F.J.
  Laros).
- Discard `None` values when writing.


Version 0.2.0
-------------

Released on September 2nd 2013.

- Auto scale tracks in distance calculation if needed (the metrics in
  `wiggelen.distance` are not defined on the (0, 1) interval).
- Add min,posmin,max fields to track index.
- Optionally consider edges in `wiggelen.fill` (`only_edges` argument).
- Introduce the `plot` module for visualizing tracks.
- Rename command line ``visualize`` function to ``plot``.


Version 0.1.6
-------------

Released on August 8th 2013.

- Support `fixedStep` definitions without `step` argument. This is not valid
  by the spec, so a practical consideration. Fixes
  `issue #1 <https://github.com/martijnvermaat/wiggelen/issues/1>`_.


Version 0.1.5
-------------

Released on July 21st 2013.

- Optional track name (`-n` or `--name`) and description (`-d` or
  `--description`) for command line functions.
- Command line argument `-n` or `--no-indices` for `merge` has been
  renamed to `-x` or `--no-indices`.
- Slight performance improvement in parsing.


Version 0.1.4
-------------

Released on July 15th 2013.

- Fix parsing tracks in fixedStep mode.
- Intervals BED track is now correctly written tab-delimited.
- Fix distance module on Python 3.2+.


Version 0.1.3
-------------

Released on June 11th 2013.

- Fix distance calculation on values below threshold. Positions where both
  values are below the given threshold are ignored.


Version 0.1.2
-------------

Released on May 6th 2013.

- Coverage intervals. Module `intervals` implements extraction of coverage
  intervals from walkers and writing them to BED files. Coverage intervals
  with an optional value threshold can be written for any wiggle track to a
  BED file using the command line `coverage` command.
- Add name and description arguments to `write` (Jeroen Laros).
- Fix dependencies declaration in setup.py (only affects Python 2.6).


Version 0.1.1
-------------

Released on April 27th 2013.

- Fix installation from PyPi (``README.rst`` was missing in sdist).


Version 0.1.0
-------------

Released on April 26th 2013.

First public release.
