Stpipeline

* st_qa.py generate expression heatmap plots
* Fixed a minor bug in the computation of the saturation curves
* adjust_matrix_coordinates now does not update the coordinates by default
* adjust_matrix_coordiantes works with the latest ST Spot detector format
* small updates in the fastq merging script
* relaxed a bit the restriction checks for some parameters

* Added extra scripts:
- merge_bcl : merge BCL files based in patterns
- filter_gene_type_matrix : filter gene in output data based on Ensembl gene types
* Bumped Pysam and HTSeq

* Small update to make the PIP installation more robust

* Small update to make the PIP installation more robust

* Optimized the counting of UMIs by strand, start-pos and offset

* Fixed a typo in one of the parameter that caused the pipeline to not run