Stpipeline

* Added parameter for strandness in annotation (yes by default)
* Simplified a bit the quality trimming step (do not account for user input trimmed bases)

* Added stats for annotated reads
* Replaced shelve dict for sqldict
* Fixed some small bugs in the annotation

* Removed the pair mode keep option
* Removed un-neccessary pair mode and mapped checks
after alignment

* Added option to do the STAR 2 pass mode
* Removed option to run pipeline without IDs
* Speed improvements
* Perform demultiplex after mapping
* No attaching the barcode to reverse reads
* Removing some parameters
* Some improvements in stDataPlotter
* Option to use BAM format
* Removed annotation filtering step
* Removed forward trimming parameters
* Output gene names even with ENSEMBL

* Small memory improvements
* Updates in plotting script

* End coordinates now contain the whole read length
* Make annotation strand aware (reverse)
* Updated to STAR 2.5