Removed loading of (putatively wrong) BSgenome package in the StrandPhaseR wrapper, it is loaded in StrandPhaseR itself anyway

Update GenomicAlignments package to 0.14, the previous environment caused the following problem in StrandPhaseR:

Warning message:
multiple methods tables found for ‘rglist’
Working on chromosome chr2
 Loading data for 58 WCregionsError in validObject(.Object) :
  invalid class “GAlignments” object: undefined class for slot "NAMES" ("characterORNULL")
Calls: strandPhaseR ... phaseChromosome -> loadMatrices -> bamregion2GRanges
Execution halted

Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline which added heat maps to simul rule

Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline including new heat_map plots from Maryam