Stpipeline

* Outputted reads JSON now only has the portion of the read that was used to map
* Cutadapt is integrated but only using the quality trimming for now
* Internal refactoring and optimizations

* Added small unit-test for molecular barcodes
* Added more molecular barcodes algorithms (using a naive one for now)
* Fixed small issues in JSON parsing libraries

* Rewrite createDatasets.py
* Clean up repository and deprecated files
* Change the unit-test library and structure
* Refactor the unit-test (use pipeline API instead of command line calls)
* Ensure unit-test remove tmp files when failing
* Add better error handling
* Add unit-test for Molecular Barcodes
* Add Molecular Barcodes functionality
* General refactor and clean up
* Add invoke options (clean, build, install)
* Fix an important bug in createDatasets that caused incorrect
computation of reads counts

* Improved installers
* Small bug fixes
* Added basic uni-test to do a run of the pipeline

* Some optimizations and bug fixes

* Fixed a error with new version of HTSeq-count that will discard more reads