CHANGES IN VERSION 1.5.2
------------------------
UPDATES

    o fixed trace names, cleanup
    o updated the code downloading SDRFs to rename seq.srdf.txt to .sdrf.txt
    o unified the functions providing default options
    o exposed the options that are used in the process
    o changed errors to warnings where process can still be completed
    o fixed improper tools detection on the external R Cloud, added 
      detection using elements in PATH.
    o simplified setting of tools options, removed the need to invoke
      initEnvironmentVariables after the options are set, made it automatic
    o updated help pages
        o composed all options related pages into "package options"
          page and "processing options" page. Exposed all options.
        o removed the initEnvironmentVariables
        o removed outdated references


CHANGES IN VERSION 1.5.1
------------------------

UPDATES
    o improved error handling within the ArrayExpressHTS
    o added stop.on.warnings that allows detection of possible failures 
      earlier. However if used it would narrow the amount of experiments 
      that can be successfully processed.
    o added log.error instead of log.info where necessary
    o reorganised pipeline options, made them visible to users in the command syntax.
    o reorganised R Cloud parameters into a single set of visible/usable options
    o made the pipeline automatically detect "Organism" from SDRF and filter using 
      a selected value.
    o reworked reading from SDRF to cover most of the "flexible formatting" cases
    o improved creation of R Cloud computation cluster, widened usage of retries.
    o added proper functions to work with environment variables
    o updated package help pages
    o updated the annotation processing following Ensembl update.
    o updated help pages, descriptions and references
    o updated package vignette documentation
        o slightly reorganised the structure of the document
        o rewritten some sections
        o added a few new sections
        o added examples where needed

    o reimplemented problematic searching and downloading of .seq.sdrf.txt files
    o fixed problematic handling of "NA" or "missing" nominal length values from ENA
    o made a number of reference preparation tasks be able to run in parallel and
    not affect each other. 
    o fixed the "count" method to properly read fields of bam files


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