Changes in version 1.40.0                        

USER-VISIBLE CHANGES

    o   count bam alignments with coordinates but flag 'unmapped' (e.g. generated by hisat2) as mapped, so that qCount, qQCReport and alignmentStats are consistent

                       Changes in version 1.34.0                        

USER-VISIBLE CHANGES

    o   removed automatic downloading and installation of BSgenome references

    o   added option to parallelize qExportWig

                       Changes in version 1.30.0                        

NEW FEATURES

    o   added binSize argument for qProfile

                       Changes in version 1.24.0                        

NEW FEATURES

    o   added support for spliced alignments using HISAT2 (via Rhisat2 package)

    o   migrated from Rsamtools to Rhtslib C library for operations on bam files

    o   migrated unit test from RUnit to testthat

    o   ignore reference deletions (BAM_CDEL) in qCount(..., reportLevel = "junction")

                       Changes in version 1.10.0                        

NEW FEATURES

    o   qExportWig gained createBigWig argument and can now create bigWig files directly

    o   qQCReport now also produces base quality plots for bam-file projects by sampling reads from the bam files

    o   qCount, qProfile and qExportWig have gained a includeSecondary argument to include/exclude secondary alignments while counting

                        Changes in version 1.8.0                        

PUBLICATION

    o   A paper describing the QuasR package has been published (see citation("QuasR")):
	Gaidatzis D. et al., Bioinformatics, 2015. doi: 10.1093/bioinformatics/btu781

NEW FEATURES

    o   started implementing support for BiocParallel, allowing QuasR to also run on batch clusters
	(support is currently limited to qQCReport)

                        Changes in version 1.4.0                        

NEW FEATURES

    o   new arguments mapqMin and mapqMaxm in qCount, qProfile, qMeth and qExportWig allow to select alignments based on mapping quality

    o   qAlign gains checkOnly argument which allows checking for existing alignments without triggering new alignments in case of missing ones

                        Changes in version 1.2.0                        

NEW FEATURES

    o   new miRNA-seq sample data; vignette has now workflows for ChIP-seq, RNA-seq, smRNA-seq/miRNA-seq, Bis-seq and allele-specific analysis

    o   qMeth can report methylation states for individual molecules (reportLevel="alignment")

    o   qCount/qProfile gain argument to ignore spliced reads in counting

                        Changes in version 1.0.0                        

INITIAL RELEASE

    o   ChIP-seq with support for single-end, paired-end and allele specific samples

    o   RNA-seq with support for spliced alignment, single-end, paired-end and allele specific samples

    o   Bis-seq with support for single-end, paired-end and allele specific samples