Changes in version 1.2.0                        

  - New event types: alternative transcription start and end sites
    (find_atss(), find_ates()) and spliced introns (find_si()).
  - New input option: prepare_exons_by_partition() builds the input from
    two user-defined sets of transcripts (up and down). Unlike
    prepare_exons(), it does not need DTU results.
  - get_seq() extracts exon sequences against a genome.
  - Plotting functions for event results: plot_transcripts(),
    plot_transcripts_by_gene(), plot_transcripts_by_pair(),
    plot_transcript_lfc() and event_palette().
  - Long-form aliases for every finder, e.g. find_skipped_exons().
  - find_se(), find_ie(), find_mxe() and find_all_events() pass extra
    arguments on to GenomicRanges::findOverlaps().
  - Results carry event_type, event_tx_id, event_estimate and
    event_<col> for any additional_columns.
  - The default type is now "over"; "boundary" matches only the splice
    site facing the candidate; and "in" is renamed "identical".

                        Changes in version 1.1.5                        

  - Added plotting functions for event results: plot_transcripts(),
    plot_transcripts_by_gene(), plot_transcripts_by_pair(),
    plot_transcript_lfc() and event_palette() (require ggplot2).
  - Added find_si() for spliced introns, the reverse of find_ri().
  - The default type of find_se(), find_ie(), find_mxe() and
    find_all_events() is now "over" (was "boundary").
  - type = "boundary" now matches only the splice site of each flanking
    exon that faces the candidate exon, on either strand.
  - The "in" match type is renamed "identical".
  - find_se(), find_ie(), find_mxe() and find_all_events() pass extra
    arguments on to GenomicRanges::findOverlaps(), e.g. minoverlap = 5L.
  - plyranges moved to Depends, so it is attached with splicelogic.

                        Changes in version 1.1.4                        

  - Added prepare_exons_by_partition() for building input from two sets
    of transcripts, without needing a estimate column from a DTU
    analysis.
  - Added find_atss() and find_ates() for detecting alternative
    transcription start and end sites. Both are included in
    find_all_events().
  - Added find_si() (alias find_spliced_introns()), the reverse of
    find_ri(): an intron that an up transcript splices out but a down
    transcript retains. find_ri() gains an inverse argument, as
    find_se() has for find_ie(). Included in find_all_events().
  - find_a5ss() and find_a3ss() now label events per moved boundary, so
    an exon that moves both of its boundaries is reported as both an
    a5ss and an a3ss.
  - The default type of find_se(), find_ie(), find_mxe() and
    find_all_events() is now "over". "boundary" now requires the flank
    to share its inner boundary — the splice site facing the candidate —
    rather than either its start or its end, and is strand-aware. The
    "in" match type is renamed "identical". Extra arguments (...) are
    passed on to GenomicRanges::findOverlaps() when matching flanking
    exons.
  - Added get_seq() to extract exon sequences from a GRanges against a
    genome.
  - Results now carry event_type, event_tx_id and event_estimate, and
    any columns registered via additional_columns are propagated to the
    partner transcript with an event_ prefix.
      - Added long-form aliases for every finder (find_skipped_exons(),
        find_included_exons(), find_mutually_exclusive_exons(),
        find_retained_introns(),
        find_alternative_5_prime_splice_sites(),
        find_alternative_3_prime_splice_sites(),
        find_alternative_transcription_start_sites(),
        find_alternative_transcription_end_sites()).

                       Changes in version 0.99.0                        

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