CHANGES IN VERSION 1.0.3
-------------------------
o Changed GenomicFeatures::makeTranscriptDbFromUCSC to
    GenomicFeatures::makeTxDbFromUCSC
o In vignette added Rsamtools:: before the BamFile function


CHANGES IN VERSION 1.0.2
-------------------------
o Added slope=1 in geom_abline
o Call to ggplot on GRanges without ggbio::ggplot

CHANGES IN VERSION 0.99.7
-------------------------
o In riboSeqFromBAM function capture.output called with utils::

CHANGES IN VERSION 0.99.6
-------------------------
o In codonPCA functions prcomp and kmeans called with stats::

CHANGES IN VERSION 0.99.5
-------------------------
o Added @return for roxygen comment in printPCA.R
o Updated packages IRanges and BSgenome.Mmusculus.UCSC.mm10 before check.

CHANGES IN VERSION 0.99.4
-------------------------
o Non-null coverage values define the percentage of best expressed CDSs.
o New function: readsToReadStart -
    it builds the GRanges object of the read start genomic positions
o Acronym BAM used instead of bam
o Correction of read start coverage (readStartCov) for the reverse strand
o Title in Description in Title Case
o Typos corrections in vignette.
o Style inconsistencies solved:
    = replaced by <- outside named arguments
    No space around “=” when using named arguments to functions. This: somefunc(a=1, b=2)
    spaces around binary operators
    a space after all commas
    use of camelCase for both variable and function names
        ORFrelativePos -> orfRelativePos
o Replaced 1:length(x) by seq_len(length(x))
o Replaced 1:nrow(x) by seq_len(NROW(x))
o Replaced trailing white spaces with this command: 'find . -type f -path './*R' -exec perl -i -pe 's/ +$//' {} \;'
o countsPlot, histMatchLength, plotSummarizedCov:
    no longer print directly the graphs. Instead they return a list of graphs.
o Replaced 'class()' tests by 'inherits' or 'is'.
o The codonPCA function no longer prints the PCA graphs sequantially.
    The 5 PCA graphs are returned, together with the PCA scores.
o New function printPCA prints the 5 PCA plots produced by codonPCA.
o A BAM file is now available in the inst/extdata ctrl_sample.bam.
    It is used in the testriboSeqFromBAM testthat

CHANGES IN VERSION 0.99.3
-------------------------
o Correction of a infinite loop in function riboSeq_fromBam

CHANGES IN VERSION 0.99.2
-------------------------
o Modified the vignette: small corrections of the explanatory text.
o Added testthat tests for the following functions:
    test-aroundPromoter.R,
    test-riboSeq_fromBAM.R,
    test-readStartCov.R

o Introduced the 4 spaces tabulation
o Reduced the percentage of lines > 80 characters to 2%
o Added imports in the Namespace for the proposed packages or methods
o New R version: 3.2.2 and bioconductor packages update

CHANGES IN VERSION 0.99.1
-------------------------
o Added biocViews:
    Sequencing,
    Coverage,
    Alignment,
    QualityControl,
    Software,
    PrincipalComponent
o Added testthat tests for the following functions:
    test-aroundPromoter.R,
    test-riboSeq_fromBAM.R,
    test-readStartCov.R

o Introduced the 4 spaces tabulation
o Reduced the percentage of lines > 80 characters to 2%
o Added imports in the Namespace for the proposed packages or methods

v.0.99.0 Initial release.
-------------------------