Changes in version 1.5.2 (2020-12-04)                  

  - Updated code that queries Ensembl for new version of biomaRt.
  - Make sure there're no NAs in tr2g_intron when chrs_only = TRUE.
  - Bypassed issue in BSgenome::getSeq in get_velocity_files when genome
    is DNAStringSet.

                 Changes in version 1.1.4 (2020-04-23)                  

  - Now tr2g_* functions can also extract transcriptomes.
  - By default, tr2g_* functions write the tr2g.tsv to disk.
  - Write filtered GTF and GFF3 files.
  - List of available gene and transcript biotypes from Ensembl can be
    queried by data().
  - RefSeq GFF3 annotations can now be used in tr2g_gff3.

                 Changes in version 1.1.3 (2020-04-06)                  

  - Allow filtering gene and transcript biotypes in tr2g and
    get_velocity_files
  - Allow removing scaffolds and haplotypes from genome annotations for
    tr2g

                 Changes in version 1.1.2 (2020-02-06)                  

  - Removed RcppParallel and data.table dependencies, and hence all C++
    multithreading
  - Added knee_plot function
  - Changed default in read_count_output to tcc = FALSE

                 Changes in version 1.1.1 (2020-01-29)                  

  - Sort GRanges for RNA velocity to make sure that exons are in the
    right order; split no longer sorts within each element of
    GRangesList.
  - Export subset_annot, which makes sure that all chromosomes in the
    annotation are present in the genome prior to transcriptome
    extraction.

                Changes in version 0.99.25 (2019-09-11)                 

  - Added message to indicate when get_velocity_files is extracting
    exon-exon junctions.
  - Restored "separate" to be default isoform_action in
    get_velocity_files.

                Changes in version 0.99.24 (2019-09-06)                 

  - When sorting tr2g from file, now the file must be formatted in ways
    required by bustools.

                Changes in version 0.99.23 (2019-09-06)                 

  - Previous two version bumps did not accompany changes; those were
    used to trigger rebuilds on Bioconductor.
  - Added the functionality to use L-1 (L is read length) bases around
    exon-exon junction to better distinguish between spliced and
    unspliced transcripts for RNA velocity.
  - Fixed serious problem with get_velocity_file that counted reads
    mapping to exons of length between L-1 and 2(L-1) as from unspliced
    transcript. This was done by an reimplementation of the method to
    get flanked intronic ranges.
  - Changed default isoform_action to "collapse".
  - Make sure that all transcripts in tr2g.tsv from get_velocity_files
    are in the transcriptome.

                Changes in version 0.99.20 (2019-08-26)                 

  - Addressed Bioconductor review.

                Changes in version 0.99.19 (2019-07-23)                 

  - Finished get_velocity_files to generate files required for kallisto
    | bustools RNA velocity.

                 Changes in version 0.99.0 (2019-06-21)                 

  - Submitted package to Bioconductor for review