Samsift

Fixes

* Don't modify SAM headers in order to avoid problems with the novel PySAM API

First Zenodo release.

Improvements

* Optimization (5x speed-up for simple filters).

New

* Add samsift-norm-sam (normalization of SAM file to facilitate their comparison).

Fixes

* Fix a bug in the internal cache (keeping old tags).

New

- Add an initialization parameter (`-0`).
- Add the `PG` tag to the output.
- Add modes of handling errors.
- Add support for Python 3.2-3.4.
- Add multiple examples of SAMsift usage.
- Add soft-clipped versions of variables (SEQs, QUALs, and QUALsa).


Improvements

- Support simultaneously both old and new PySam versions.
- Test the entire package using Travis.


Fix

- Fix a major bug with parsing command-line arguments containing spaces.
- Fix many other bugs.

The first public release.