Stpipeline

* Removed parallel code for un-necessary parts
* Added option to provide saturation points

* Improved the st_qa.py script
* Few small improvements in the annotation step
* Added support to use a transcriptome (--transcriptome)

* Fixed a error in the parameters

* Added option to disable the barcode demultiplexing step
* Added option to disable the UMI filtering step

* Made the parsing of unique UMIs gene by gene and parallel
* AdjacentBi is now the default method for UMI counting
* Made the trimming function output the trimmed R2 in BAM format with the barcode and UMI
* Made the mapping function works with a BAM file as input (latest STAR release)
* Made the annotation function parallel
* Made the quality step parallel
* Improvements in speed and memory (constant memory use)
* The STAR genome loading strategy can be now set
* Added an affinity based method to cluster UMIs
* Added option to set the STAR BAM sort memory limit

* Fixed a bug that will output the matrix of counts inverted