Changes
* Added Python 3 compatibility
* Removed gtf format input for TE annotations, which removed a holdover behavior where subfamily-level clustering was being done if not using a prebuilt index for TEs
* Thanks to Savytska Natalia for spotting that
* Streamlined and removed unused code inherited from TEtranscripts
* Updated the `--stranded` parameter to utilize `forward` instead of `yes` for stranded libraries sequenced in the direction of transcribed RNA.
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
* Allow `--verbose` to be invoked without arguments