CHANGES IN VERSION 1.5.3
-------------------------
o Corrected a bug in utils.R, readStartCov1Aln function. 
	normRange(listReadStartCov, fixedInterval), in case ixReverse null


CHANGES IN VERSION 1.5.2
-------------------------
o Down-sampled the ctrlGAlignments.rda object from the data folder
o Changed conflicting sweave-knitr in the vignette


CHANGES IN VERSION 1.5.1
-------------------------
o For the vignette the example bam files have been down-sampled and added to the extdata folder
o Changed the vignette accordingly

CHANGES IN VERSION 1.1.6
-------------------------
o replaced IRanges::as.table since it is not exported by IRanges anymore, with as.table
o motifSize in countShiftReads and codonInfo can be only 3, 6 or 9
o in countShiftReads and codonInfo, motifs of size 6 or 9 correspond to overalpping
    windows, sliding 1 codon at a time
o in countShiftReads, for motifSize = 6, the P-site is the first codon of the 2
    it means that only the reads of the 1st codon in the 2 codon-motif are counted
o in countShiftReads, for motifSize = 9, the P-site is the second codon of the 3
    it means that only the reads of the 2nd codon in the 3 codon-motif are counted
o adapted the RiboProfiling.Rnw to explain the treatment of motifs of codons (1, 2, or 3)
    as opposed to the previous treatment of unique codons.
o changed S4Vectors::elementLengths to S4Vectors::elementNROWS in riboSeqFromBAM,
    aroundPromoter



CHANGES IN VERSION 1.1.5
-------------------------
o replaced GenomicRanges::assays since it is not exported by GenomicRanges anymore,
    by SummarizedExperiment::assays, and importFrom

CHANGES IN VERSION 1.1.4
-------------------------
o replaced GenomicRanges::assays since it is not exported by GenomicRanges anymore,
    by assays

CHANGES IN VERSION 1.1.3
-------------------------
o function "codonInfo" modified
    optimized for motifs of 1 or 2 consecutive codons
o getCodons (utils), countShiftReads, and codonInfo functions modified
    it allows to look at sequence motifs not only for codons (3 nucleotides) but for other sizes as well
    motifSize parameter has been added to these functions to specify the number
    of nucleotides on which to compute usage and coverage.
o function "readsToReadStart" replaced by "readsToStartOrEnd"
    this new function focuses not only the read 5' (start) but also the read 3' (end)
o In riboSeqFromBAM added a parameter offsetStartEnd. It specifies if the offset
    is to be computed on the 5' or 3' of the read.


CHANGES IN VERSION 1.1.2
-------------------------
o added slope to geom_abline function


CHANGES IN VERSION 1.1.1
-------------------------
o Added RiboSeq biocViews

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.
-------------------------
