Atropos

* Migrate to Versioneer for version management.
* Enable stderr as a valid output using the '\_' shortcut.
* Add ability to specify SAM/BAM as input format.
* Add option to select which read to use when treating a paired-end interleaved or SAM/BAM file as single-end.
* Remove restrictions on the use of --merge-overlapping, and enable error correction during merging.
* We are beginning to move towards the use of commands for all operations, and read-trimming now falls under the 'trim' command. Currently, calling atropos without any command will default to the 'trim' command.
* When InsertAdapterCutter.symmetric is True and mismatch_action is not None, insert match fails, at least one adapter match succeeds, and the adapter matches (if there are two) are complementary, then the reads are treated as overlapping and error correction is performed. This leads to substantial improvements when one read is of good quality while the other is other is of poor quality.

* Fixed missing import bug in 'detect' command.
* Added estimate of fraction of contaminated reads to output of 'detect' command.
* Optionally cache list of known contaminants rather than re-download it every time.

* Implemented \_align.MultiAligner, which returns all matches that satisfy the overlap and error thresholds. align.InsertAligner now uses MultiAligner for insert matching, and tests all matches in decreasing size order until it finds one with adapter matches (if any).
* Major improvements to the accuracy of the 'detect' command.
* Added options for how to correct mismatched bases for which qualities are equal.
* Added option to select a single pair of adapters from multiple sequences in a fasta file.
* Fixed report when insert-match is used.
* Fixed several bugs when using the "message" progress bar (thanks to Thomas Cokelaer!).
* Fixed a segmentation fault that occurs when trying to trim zero-length reads with the insert aligner.
* Sevaral other bugfixes.

* Add options to specify max error rates for insert and adapter matching within insert aligner.
* Add new command to estimate empirical error rate in data set from base qualities.

* Add ability to correct errors during insert-match adapter trimming.
* Implement additional adapter-detection algorithms.
* Fix bug where default output file is force-created in parallel-write mode

* Clarify and fix issues with bisulfite trimming. Notably, rrbs and non-directional are now allowed independently or in combination.