Cutadapt

-----------------

* add ``--too-short-output`` and ``--untrimmed-output``, based on patch by Paul Ryvkin (thanks!)
* add ``--maximum-length`` parameter: discard reads longer than a specified length
* group options by category in ``--help`` output
* add ``--length-tag`` option. allows to fix read length in FASTA/Q comment lines
(e.g., ``length=123`` becomes ``length=58`` after trimming) (requested by Paul Ryvkin)
* add ``-q``/``--quality-cutoff`` option for trimming low-quality ends (uses the same algorithm
as BWA)
* some refactoring
* the filename ``-`` is now interpreted as standard in or standard output

-----------------

* Change default behavior of searching for an adapter: The adapter is now assumed to
be an adapter that has been ligated to the 3' end. This should be the correct behavior
for at least the SOLiD small RNA protocol (SREK) and also for the Illumina protocol.
To get the old behavior, which uses a heuristic to determine whether the adapter was
ligated to the 5' or 3' end and then trimmed the read accordingly, use the new
``-b`` (``--anywhere``) option.
* Clear up how the statistics after processing all reads are printed.
* Fix incorrect statistics. Adapters starting at pos. 0 were correctly trimmed,
but not counted.
* Modify scoring scheme: Improves trimming (some reads that should have been
trimmed were not). Increases no. of trimmed reads in one of our SOLiD data sets
from 36.5 to 37.6%.
* Speed improvements (20% less runtime on my test data set).

-----------------

* Useful exit codes
* Better error reporting when malformed files are encountered
* Add ``--minimum-length`` parameter for discarding reads that are shorter than
a specified length after trimming.
* Generalize the alignment function a bit. This is preparation for
supporting adapters that are specific to either the 5' or 3' end.
* pure Python fallback for alignment function for when the C module cannot
be used.

-----------------

* Support gzipped input and output.
* Print timing information in statistics.

-----------------

* add ``--discard`` option which makes cutadapt discard reads in which an adapter occurs

-----------------

* (more) correctly deal with multiple adapters: If a long adapter matches with lots of
errors, then this could lead to a a shorter adapter matching with few errors getting ignored.