CHANGES IN VERSION 1.3.1
------------------------

NEW FEATURES

    o Added test dataset, which is a cut version of E-GEOD-16190 experiment
    o Added normalization of the reference folder
    o Added automatic fixing of reference .fai index, namely duplicated chromosome entries
    o Added automatic detection of quality scale where possible
    o Added and option to specify quality scale for custom experiments
    o Performed performance and memory optimization
    o Removed options$reference_version. Since the pipeline allows processing of 
      multi-species datasets, a single version cannot fit into multiple organism 
      paradigm. The pipeline always runs on the latest version of reference. 
      Support for custom versions can be added upon request.
    o Added memory monitoring

BUG FIXES

    o Fixes to accommodate changes in Ensembl interfaces, required for 
      preparation of reference and annotation data.
    o Fixes to accommodate changes in ENA interfaces, required for querying 
      metadata  & downloading datasets for ArrayExpress experiments.
    o Fixed examples in prepareReference help page
    o Fixed ArrayExpressHTSFastQ scenario without .sdrf
    o Fixed production of final alignment report


CHANGES IN VERSION 1.3.0
------------------------

     o No changes. Version changed due to package propagation.


CHANGES IN VERSION 1.0.1
------------------------

NEW FEATURES

    o added prepareAnnotation and prepareReference functions
    o reworked the discovery of reference data
    o updated the package after upgrading R and related packages on the EBI R-Cloud

BUG FIXES

    o Fixed computation of insert size for paired end experiments
    o Fixed fltbam tool that was not part of the pipeline and could not be invoked
    o Fixed plot_scatter_samples calling to_expressionset with wrong argumenta
    o Fixed problems with graphics after upgrade of R and graphics subsystem