Version 1.3.2 (2022-10-25)
+ Announcing that NxtIRFcore will be superceded by SpliceWiz from Bioc 3.16 onwards.

Changes in version 1.2.1/1.3.1 (2022-06-22)
+ Bugfix for BuildReference: ignores "N" bases when translating codons (instead of returning an error)
+ Bugfix for BuildReference: more versatile handling of cache locations for BiocFileCache
  
Changes in version 1.1.1 (2022-01-11)
+ Bugfix for NxtSE constructor.
+ Bugfix for Consistency filter: previously an "average" filter was used, such
that upstream / downstream filter triggers counted for 0.5, whereas it added 1.0
if both up/downstream filters were triggered. From 1.1.1 onwards, 1.0 is added when either upstream or downstream consistency filter is triggered.
+ Added two new annotation-based filters: Terminus and ExclusiveMXE. See ?NxtFilter for details
+ Annotated retained introns `RI` are defined by any intron that is completely overlapped by a single exon of any transcript. They are calculated as binary events, i.e. as PSI between RI and specific spliced intron, and do not consider overlapping splice events (unlike `IR` events, which are calculated for all other constitutive introns)

Changes in Version 1.1.0
+ Initial devel release for Bioconductor 3.15

Changes in version 0.99.12 (2021-10-26)
+ Fixed bug in MakeSE() and CoordToGR()

Changes in version 0.99.10 (2021-10-20)
+ Accounts for when NxtIRFdata cannot fetch data from ExperimentHub

Changes in version 0.99.9 (2021-10-20)
+ Added GetCoverageBins()
+ Add warning in IRFinder if coordinate sorted BAM file takes too long to run.
+ Fixed missing coverage data at both ends of plot track.

Changes in version 0.99.8 (2021-10-13)
+ Fixed memory leak when writing COV files

Changes in version 0.99.6 (2021-10-12)
+ Added GetCoverageRegions() which calculates the mean coverage of each region
in a given GRanges object
+ Added BAM2COV() which calculates and creates COV files from BAM files

Changes in version 0.99.2 (2021-10-07)
+ Fixed bug in Find_FASTQ

Changes in version 0.99.0 (2021-09-29)
+ Bioconductor Release