========= Changelog ========= .. Newest changes should be on top. .. This document is user facing. Please word the changes in such a way .. that users understand how the changes affect the new version. ----------- v0.2.15-dev ----------- + Fix a possible security vulnerability when using the `GTGT_CACHE` + Add categories and descriptions to the external resources page ------- v0.2.14 ------- + Fix a bug comparing empty features + Fix a bug where a therapy restoring part of a feature was not recognized ------- v0.2.13 ------- + Collapse the unchanged annotations in the frontend + Hide empty sections in the frontend + Only show relevant therapies by default. A therapy is relevant if it modifies at least one input variant, or improves at least one annotation ------- v0.2.12 ------- + Fix a bug which caused protein domains to not be updated ------- v0.2.11 ------- + Hotfix to roll back protein domains in the frontend ------- v0.2.10 ------- + Enable support for protein domains in the frontend ------ v0.2.9 ------ + Fix a bug with analyzing non-human Ensembl transcripts + Remove the API endpoints + Remove pydantic models which were only used by the API endpoints + Refactor Provider class (used to cache API calls) + Add support for querying UCSC tracks for a given Description ------ v0.2.8 ------ + Add support for refseq (NM) transcripts ------ v0.2.7 ------ + Fix a bug where the ExonViz figure cannot be drawn at the default scale + Drop support for python 3.9 + Add support for python 3.14 ------ v0.2.6 ------ + Fix circular import with exonviz ------ v0.2.5 ------ + Group Therapies together in the html + Show a figure of the input variants in the html + Add RNA and protein variant descriptions ------ v0.2.4 ------ + Add spinner to show progress to html + Add clickable examples to the html + Add ``gtgt export`` to the command line interface + Add separate mRNA and protein features to the Transcript + Extend documentation sections of the html ------ v0.2.3 ------ + Enable skipping two adjacent exons by default + Explicitly check that the variants are specified in ``c.`` format + Refactor internal representation of variants + Reduce analysis time ------ v0.2.2 ------ + Update the analysis results to give more information on proposed Therapies + Improve type annotations + Reduce the analysis time by 50% per exon + Fix a bug where the number of changed amino acids was overestimated ------ v0.2.1 ------ + Re-use mutalyzer Description object to reduce load on Ensembl API + Drop support for Python 3.8 + Add support for Python 3.13 + Add number of remaining basepairs to the transcript comparison + Rename default annotations for clarity + Fix a bug when the specified variant partially overlaps an exon + Fix a bug when VariantValidator is not available + Check user input for errors in web interface + Rename module from GTGT to gtgt ------ v0.2.0 ------ + Rename python package from GTGT to gtgt ------ v0.1.1 ------ + Add support for re-using mutalyzer Descriptions + Add support for small deletions + Fix a bug parsing VariantValidator payload + Add web interface using Flask ------ v0.1.0 ------ + Change the transcript endpoint to use POST and a TranscriptId model + Use genomic location for ClinVar link + Add support for Ensembl transcripts on the links endpoint + Refactor and simplify the BedModel + Validate HGVS is valid before querying Variant Validator + Change the links endpoint to use POST and HGVS + Add FastAPI endpoint for comparing transcripts + Add FastAPI endpoint for skipping exons + Add Flask web app + Drop support for Python 3.8 + Add support for python 3.13 ------ v0.0.2 ------ + Add FastAPI endpoint for transcripts and links + Add link to stringDB + Add link to gnomAD + Add API endpoint /links/ to fetch URL's for external references + Fetch knownGene track from UCSC + Fetch transcript information from Ensembl ------ v0.0.1 ------ + Add class for Transcripts + Validate that the input is valid Bed format + Add class for Bed format + Initial commit