Tetranscripts

Changes
- Fix Docker/Singularity container to properly install `locfit` module required for `DESeq2` (Issue 120)
- Many thanks to molikd for the patch.

Changes
- Provided support for Docker/Singularity
- Many thanks to molikd for this update.

Minor changes
- Added parameter `--outdir` to allow specification of output directory (117)
- The output directory must already exist
- Updated `argparse` requirement as it is now a standard Python library (111)
- Enable _independent filtering_ by default in `DESeq2` script (114)

Minor fix
* Allow `--verbose` to be invoked without arguments

- No changes from version 2.2.1

Changes
- Added Python 3 compatibility (as requested by issue 61)

Minor changes
- Minor fixes to read apportioning
- Minor fixes to correctly handle SAM as input
- Minor fixes to features list when running on unstranded libraries

Changes
* Updated the `--stranded` parameter to utilize `forward` instead of `yes` for stranded libraries sequenced in the direction of transcribed RNA.
* Clarified library prep that would utilize `--stranded forward` parameter
* Thanks to Kimberley Billingsley for spotting the mistake.