CHANGES IN VERSION 1.14.0 (2025-10-26)
--------------------------------------

BUG FIXES

    o Bugfix on annotaTEs() to handle the case then LC_TIME is other than C or English, raised in issue #8. A few fixes on documentation links.

    o Switch some imports from GenomeInfoDb to the new Seqinfo package.

CHANGES IN VERSION 1.14.0 (2025-04-14)
--------------------------------------

USER VISIBLE CHANGES

    o In the call to 'annotaTEs()' the user may provide ther parser function to the parameter 'parsefun' as a function name in a character string without triggering an error.

CHANGES IN VERSION 1.10.0 (2024-04-27)
--------------------------------------

USER VISIBLE CHANGES

    o Annotation metadata is now propagated to parameter and resulting SummarizedExperiment objects, which can be retrieved using  'mcols(features(x))' and 'mcols(rowRanges(x))' methods, respectively.

    o The TE subclass annotation getter functions 'getLTRs()', 'getLINEs()', 'getSINEs()' and 'getDNAtransposons()' work now with both, parameter and resulting SummarizedExperiment objects.

    o Manual pages and the vignette have been updated to illustrate the previous changes.

BUG FIXES

    o Several bug fixes, mostly in how annotation metadata was stored and propagated.

CHANGES IN VERSION 1.6.0 (2023-04-20)
-------------------------------------

USER VISIBLE CHANGES

    o Improvement of the accuracy of the atena expression quantification method.

    o Fixed numerical instability in TEtranscripts method.

    o Added function (.matchSeqinfo) to harmonize seqinfo() of object with alignments and object with feature annotations.

    o Implemented 'OneCodeToFindThemAll' annotation parser for RepeatMasker annotations.

    o Implemented 'atena' annotation parser for RepeatMasker annotations.

    o Added examples in the vignettes of TE annotation preprocessing steps using the implemented parsers.

    o Changed default value of geneFeatures to NULL in the parameters objects.

BUG FIXES

    o Fixed bug for not properly paired reads.


CHANGES IN VERSION 1.6.0 (2023-04-20)
-------------------------------------

USER VISIBLE CHANGES

    o Improvement of the accuracy of the atena expression quantification method.

    o Fixed numerical instability in TEtranscripts method.

    o Added function (.matchSeqinfo) to harmonize seqinfo() of object with alignments and object with feature annotations.

    o Implemented 'OneCodeToFindThemAll' annotation parser for RepeatMasker annotations.

    o Implemented 'atena' annotation parser for RepeatMasker annotations.

    o Added examples in the vignettes of TE annotation preprocessing steps using the implemented parsers.

    o Changed default value of geneFeatures to NULL in the parameters objects.

BUG FIXES

    o Fixed bug for not properly paired reads.

CHANGES IN VERSION 1.4.0 (2022-11-31)
---------------------------------------

USER VISIBLE CHANGES

    o Implemented 'choose', 'average' and 'conf' reassignment modes in Telescope method.
    o Creation of a 4th expression quantification method, called the atena method.
    o Modified 'ovUnion' method to address alignments overlapping > 1 feature.
    o Implemented 'OvIntersectionStrict' overlapping method.
    o Adapted annotaTEs() function to new RepeatMasker annotations in AnnotationHub.
    o Changed coercions to dgCMatrix and lgCMatrix to go via virtual classes to comply with latest updates in Matrix version 1.4-2.

CHANGES IN VERSION 1.2.0 (2022-04-21)
---------------------------------------

USER VISIBLE CHANGES

    o Higher accuracy in TE quantification for TEtranscripts and Telescope methods.
    o Improved EM step running time.
    o New AnnotationHub resource has been added: UCSCRepeatMasker.
    o Implemented function to retrieve and parse TE annotations.

CHANGES IN VERSION 0.99.36 (2021-08-01)
---------------------------------------

USER VISIBLE CHANGES

    o Submission of the first version to the Bioconductor project.
