changelog
    version 1.5.8 - 1.5.9
        - bugfix in seeFastqPlot caused by recent change in ggplot2
        - fix in fstats component of seeFastq

    version 1.5.6 - 1.5.7
        - vignette updates

    version 1.5.5
        - fixed extendylim in plotfeatureCoverage()
        - fixed error in featureCoverage when txdb/grl was created from gff with scaffolds not containing any genes

    version 1.5.0 - 1.5.4
        - doc updates
        - git mirror setup
        - fixed genFeatures for txdb instance from makeTxDbFromUCSC()
        - fixed genFeatures for empty range sets

    version 1.3.44 - 1.3.50
        - added predORF
        - added scaleRanges
        - optimized performance of scaleRanges
        - vignette updates
        - translational efficiency modeling with DESeq2

    version 1.3.35 - 1.3.43
        - added featureCoverage and plotfeatureCoverage
        - vignette updates
    
    version 1.3.31 - 1.3.35
        - added Ribo-Seq function: genFeature
        - added Ribo-Seq functions: featuretypeCounts and plotfeaturetypeCounts
        
    version 1.3.23 - 1.3.30
        - vignette updates
        - updated ChIP-Seq workflow
    
    version 1.3.21 - 1.3.22
        - added writeTargetsRef and mergeBamByFactor
    
    version 1.3.17 - 1.3.10
        - Converted main vignette to R Markdown
        - Instructions to download sample data via systemPipeRdata
        - Fix for missing systemPipeRdata on build system
        - Fix to get correct name of HTML page on Bioc page

    version 1.3.16
        - Fixed minor bug in runCommandline

    version 1.3.14 - 1.3.15
        - Fixed PE support in preprocessReads
    
    version 1.3.13
        - Included gsnap and VariantTools examples in vignette
    
    version 1.3.8 - 1.3.12
        - vignette updates 
    
    version 1.3.7
        - added sample Makefile 
    
    version 1.3.4 - 1.3.6
        - vignette updates 
    
    version 1.3.3
        - updated readComp 
        - corrected typo for systemArgs when NULL is assigned to sysma
    
    version 1.3.2
        - fixed path to BatchJob's log file location when symbolic links are used
    
    version 1.1.16
        - added functions for variant filtering and annotation
    
    version 1.1.15
        - support for GATK and BCFtools
    
    version 1.1.12-1.1.14
        - vignette/man updates
    
    version 1.1.11
        - added DESeq2 support
    
    version 1.1.9-1.1.10
        - vignette/man updates
    
    version 1.1.8
        - added preprocessReads function
    
    version 1.1.7
        - support for R-based software generating input/output files
        - support for pipelines with several system command steps
    
    version 1.1.6
        - added new *.param files
    
    version 1.1.5
        - vignette updates
    
    version 1.1.4
        - updated vennPlot

    version 1.1.3
        - added functions: overLapper, vennPlot and olBarplot
        - eliminated warning in seeFastq
    
    version 1.1.2
        - documentation update

    version 0.99.0 - 1.1.1
        - initial version on Bioconductor