GitHub repository: iobio/gene.iobio
Description: Gene.iobio vue

gene_4.10: tag_name: gene_4.10
body: **NOTE:** gene.iobio 4.10 depends on iobio-gru-backend 1.18.0, with data directory 1.12.0

Features and Bug fixes:

1. #839   New feature - Gene synonyms. The geneinfo service and gene.iobio.db associate gene names with aliases. This gene.iobio.db now has tables `gene_symbol` and `gene_alias` that are imported from the HGNC dataset `hgnc_complete_set.txt`. See repo https://github.com/iobio/geneinfo.db for details of how gene.iobio.db is built.

  - When searching for a gene name, the search will encompass gene aliases. 

    <img width="432" alt="Screenshot 2024-02-29 at 3 16 26 PM" src="https://github.com/iobio/gene.iobio/assets/8420103/1cdfec6e-2cf9-43b9-a6ef-ede256ffe4cc">

  - If a gene name is chosen that does not have transcripts for the genome build and source (refseq or gencode), the user will be warned and the app will select the gene alias that corresponds to a valid gene and transcripts for the genome build and source.
  
    <img width="333" alt="Screenshot 2024-02-29 at 3 18 49 PM" src="https://github.com/iobio/gene.iobio/assets/8420103/5ab6b005-ca4b-4574-a686-c8c65435e2d0">


2. #1042  In Variant inspect card, show HGVS names directly rather than requiring user to click on menu button. This will make copy/pasting of HGVS names easier.

<img width="375" alt="Screenshot 2024-02-29 at 3 33 59 PM" src="https://github.com/iobio/gene.iobio/assets/8420103/5de9f319-d847-4e5b-bcdf-f24d0e50790d">


3. #1052  Bug fix - Variant filter for max AF not working. When user cleared out allele frequency filter, the app was incorrectly treating this as a filter for a 0 allele frequency (not present in gnomAD). Now the app will bypass filtering on allele frequency with the field is blank in the filter dialog.

4. #1043  Bug fix - When gene source changes automatically (gencode to refseq), the label in the transcripts card doesn't reflect the gene source. This fix was part of the rework for gene aliases. Now the app will find the gene name with accompanying transcripts for a genome build and source and automatically switch to this gene.

5. #1044  Zoom and then click on variant messes up pileup in variants card. When users zoomed into a region and then clicked on a variant, the pileup reverted and all the variants were bunched together.


gene_4.9a: tag_name: gene_4.9a
body: #1047 -  Fix bug so that when 'show clinvar variants' is checked, user can add a new gene.
#1048 - Fix bugs in the gene list menu that was preventing new genes from being added when an error was encountered.
gene_4.9: tag_name: gene_4.9
body: NOTE: Features and bug fixes slated for Release 4.8 were combined with Release 4.9

### Major Features
  - #844 Integrate gene:phenotype associations
  - #165 Need to refresh gene2pheno db when HPO releases new gene-to-phenotype file 
  - #846 Variant annotations
  - Reload geneinfo db using Python script, providing end-to-end ETL solution

### Minor Features and Bug fixes
  - #899 Add gnomAD homozygous count enhancement 
  - #933 IGH gene has 2 entries in RefSeq gf 
  - #949 Defer accessing PubMed until user clicks on 'Details' 
  - #965 Regenerate genes.json 
  - #983 Transcripts menu   - MANE transcript shows as selected (in blue rectangle), even when another transcript is selected in dropdown 
  - #987 gencode should be a button  
  - #989 Gene list label should be removed when list is changed  
  - #990  Called variants gene count  
  - #1007 Variant under custom and standard filter has confusing selection behavior.  
  - #1008 Styling on significance in variant inspect card is disrupted if "uncertain significance" is selected  
  - #1009 Small yellow box with . appears when refseq selected  
  - #1010 After loading demo data, variant count in Variants tab is doubled (should be 9, shows 18) 
  - #1011 After loading demo data, first time I select a variant from variants side panel, the list refreshes 
  - #1015 Checking the 'Clinvar' track results in null ref (bug introduced with select annots feature)  
  - #1016 Clicking on a ClinVar variant in the clinvar track results in Vue.js warning about immutable props being changed  
  - #1022 Need more height for Gene disease associations in Gene  -Phenotype associations dialog. 
  - #1023 Don't show all of the search hits in the Variants side panel when launched w/i clin.iobio 
  - #1024 The phenolyzer search hits don't show on dialog 'Show more' when gene.iobio runs w/i clin.iobio 
  - #1025 The order of the custom annotations showing in VariantInspectCard should be the order that appears in the dialog for selected the annotations 
  - #1027 Hitting the 'cancel' button in SelectVariantAnnotationsDialog should not clear out all of the checked annotations  
  - #1028 The annotation values in the format field of the vcf are not showing.  
  - #1029 The SAC genotype field is listed in the "format" vcf field, but it is not available for selection in the dialog  
  - #1035 Mosaic annotations are not showing in Select Annotations dialog when clin.iobio launched from
 
gene_4.7.3c: tag_name: gene_4.7.3c
body: #1002 Handle saving/initializing of variant interpretation when variant not present in Mosaic.
gene_4.7.3b: tag_name: gene_4.7.3b
body: #988 Add filter won't allow Apply
#997 Cannot load saved analysis due to 'bindTo' problem
#998 Cannot launch analysis due to backward compatibility
gene_4.7.3a: tag_name: gene_4.7.3a
body: Emergency bug fix
- Cannot launch gene.iobio from Mosaic when index is .csi #991
gene_4.7.3: tag_name: gene_4.7.3
body: - Get rid of old dependency iobio.js #945 
- v4.7.1 Side-panel Bugs (progression and variant numbering) #934
- Remove obsolete code for local vcf and bam files #916
- Inform user why load button is disabled in Files dialog #943
- Variant detail for a called variant shows incomplete info Pedigree genotype viz (in VariantInspectCard). bug #966 
- Genes with no transcripts bug #964 
- The vertical panels in the navigation drawers are cropped for approximately 10 pixels. bug #973 
- Show transcripts in reverse order so that MANE transcript appears at top of list #976
- Clear warning from alerts when retry of PubMed, OMIM, etc results in successful response bug #977 
- Large pedigree scaling #974
gene_4.7.2: tag_name: gene_v4.7.2
body: - Can't call variants on single sample (only trios) https://github.com/iobio/gene.iobio/issues/951
- Calling variants on same gene duplicates results (prev called variants not getting cleared out) https://github.com/iobio/gene.iobio/issues/952
- Fixed silent runtime error when clicking on 'edit filter' (from left side panel, variants tab) https://github.com/iobio/gene.iobio/issues/968
- Fixed silent runtime error when loading saved analysis https://github.com/iobio/gene.iobio/issues/967
- Only cache danger summary when it has changed https://github.com/iobio/gene.iobio/issues/969
gene_4.7.1b: tag_name: gene_4.7.1b
body: - Fix styling bug so that stop analysis button is visible
- Address export .csv issues
- Inform user of missing required field (e.g. 'Please select a sample to be analyzed') when the load button is disabled in the Files dialog
- When there is a problem encountered with gene coverage, the variants should still be loaded.
Gene 4.7.1a: tag_name: gene_4.7.1a
body: Bug fix (variant export gnomad AF)
gene_4.7.1: tag_name: gene_4.7.1
body: - #924 Filtering on variants results in different set of variants when launching saved analysis vs. launching with variant set. 
- #925 Rename flagged variants heading 'Filtered variants' and 'Not found' to more descriptive terms
- #926 Maintain consistent order of filters in left hand Variants panel
- #928 Since NCBI eutils on gene fails quite often, don't show as 'warning' in app notifications.
gene_4.7: tag_name: gene_4.7
body: 1. Provide faster response times for previously saved analysis. When user saves an analysis, variant annotations are saved. When the analysis is loaded at a later time, these variant annotations are loaded into the browser's cache. Now, when the user clicks on a gene, the variants will appear in real-time, fully annotated. Also, application settings, such as customized filters, sequence coverage cutoffs, and application notifications will be saved and reloaded, so the user can continue with their analysis seamlessly. This release allows users of the public gene.iobio (https://gene.iobio.io) to save their work in a json file (by clicking on the 'Save button' in the navigation bar) and load at a later time, by clicking on  'Load.. saved analysis' and choosing the saved .json file from their local file system. Mosaic users use the 'Save analysis' feature and 'Lauch analysis' features as they did in prior releases. 
2. Mosaic users will now see variant interpretations saved back to Mosaic variants, so that when a variant is intepreted from an analysis, all Mosaic users with read permissions on the project will be able to see which variants have been marked as 'Signicant', 'uncertain significance' or 'Not significant'.
3. Error reporting has been improved significantly. Now when a failure of a backend service occurs, the user will be shown the error in the 'Notifications' (right) side panel. The navigation bar will show badges when an error has occurred and show a different badge when a warning has occurred and a different badge when a gene has insufficient coverage. Also, informational alerts will be shown, like when a new list of genes has been entered or a new phenotype-based search has returned a new gene list.

Here is a more detailed list of issues/bugs addressed in this release:

- #918 Real-time / saved data
- #919 For public gene.iobio, user should be able to save analysis and reload later with quick response times.
- #920 Improve error reporting and show errors, warnings, and info as alerts in Notifications sidebar.
- #921 Introduce transcript card
- #906 Use csi as well as tbi indexes
- #869 Need informative 'no transcripts for gene' message when gene added from 'genes list' or gene dropdown.
- #889 Genes in non-standard chromosomes error on gene coverage.
- #878 Handle new gnomAD fields in variants sets (when launched from Mosaic)
- #901 When adding genes based on phenolyzer search, previously entered genes are removed even though user specified otherwise 
- #902 Conflicting ClinVar icons
- #888 Gene shows badge of insufficient coverage, but no exons are highlighted
- #709 The transcript (dropdown button) label in the Genes panel is slow to refresh, showing old transcript from prev selected gene. 
- #923 Fix intermittent bug where first variant selected after 'analyze all' completed results in empty set of variants in variants card. 
- #886 UI doesn't properly refresh when coverage threshold is changed
- #922 Create new screencast based on latest UI and functionality introduced in gene 4.7

gene_4.6.12: tag_name: gene_4.6.12a
body: ## What's Changed
* Fix broken links in variant detail to gnomAD and dbSNP
* Cite REVEL version (v1.3)
* Add ACMG v3.2 gene panel


**Full Changelog**: https://github.com/iobio/gene.iobio/compare/gene_4.6.11...gene_4.6.12a
gene_4.6.11: tag_name: gene_4.6.11
body: - Upgrade iobio-api-client to 0.11.0 for iobio gru backend logging
- Fix null ref for Mosaic variant missing gnomAD field (when launching gene.iobio from Mosaic with a variant set)
gene_4.6.10a: tag_name: gene_4.16.10a
body: Fix bug so that genes with 'orf' can be entered in 'genes' textarea. #866
gene_4.6.10: tag_name: gene_4.6.10
body: ## What's Changed
* Fix dbSNP URL in Variants card
* Show MANE SELECT tag for transcript in Genes card


**Full Changelog**: https://github.com/iobio/gene.iobio/compare/gene_4.6.9...gene_4.6.10
gene_4.6.9: tag_name: gene_4.6.9
body: Fix Files dialog bug so that unaffected and affected sib selection is correctly reflected when load button pressed.
gene_4.6.8: tag_name: gene_4.6.8
body: 1. Refresh genes in dropdown to match latest backend gene transcripts database, loaded from refseq and gencode gffs.
2. Introduce better error reporting on genes that can't be annotated because of non-standard chromosome not present in vcf.
3. Fix so that when gene cannot be annotated in 'Analyze all', the loading gif hides and an error glyph shows beside gene.
gene_4.6.7: tag_name: gene_4.6.7
body: <img width="919" alt="Screen Shot 2022-07-19 at 2 16 04 PM" src="https://user-images.githubusercontent.com/8420103/179840421-88f9eaa6-743d-41bd-9911-4b0364b0830b.png">

**Full Changelog**: https://github.com/iobio/gene.iobio/compare/gene_4.6.6...gene_4.6.7
gene_4.6.6: tag_name: gene_4.6.6
body: 1. Use new Mosaic api for variant sets.
2. Signed URLs from public Mosaic result in warning on Load dialog; continue button does nothing. Fixed so that validation check occurs when only vcf/tbi signed URLs entered. And fixed bug so that 'Continue' closes dialog so that user can then click 'load'.
3. Fix content type to get rid of pre-flight CORS request to multialign server
When is_pedigree=false parameter is passed in from Mosaic ("Individual" was selected instead of "Family), gene.iobio should launch with this sample, ignoring the pedigree associated with this sample.
4. Fix styling so that badges on left side panel for 'Variants' and 'Genes' are not wrapping but instead appear next to the tab labels. (Firefox browser)
5. Don't collapse the expansion panel when the user clicks on 'Edit' to edit the filter
6. Add new ACMG SF V3.1 (78 genes) genes panel
gene_4.6.5: tag_name: gene_4.6.5
body: Fix Mosaic variant sets
gene_4.6.4: tag_name: gene_4.6.4
body: Makes requests to new version of annotateVariantsV2 which adds gnomAD annotations much faster, using vcfanno rather than bcftools.
gene_4.6.3: tag_name: gene_4.6.3
body: Add publication to home page and naviation menu.
gene_4.6.2 2021-09-28: tag_name: gene_4.6.2_20210928
body: ACMG v3 (73)
gene_4.6.2_20210922: tag_name: gene_4.6.2_20210922
body: Emergency bug fix - fix local file selection of vcf.gz/tbi and .cram/.crai which was broken due to incomplete backout of #761.
gene_4.6.2: tag_name: gene_4.6.2
body: Remove REVEL criterion from HIGH/MODERATE filter 
gene_4.6.1c-09-14-2021: tag_name: gene_4.6.1c-09-14-2021
body: Default behavior is to show all variants (toggle switch 'Coding variants only' defaults to off).
gene_4.6.1b (09-10-2021): tag_name: gene_4.6.1b-09-10-2021
body: Emergency bug fix for Nebula.  Default behavior in Simplified view should be to show all variants (include variants non-coding regions)
gene 4.6.1a: tag_name: gene_4.6.1a
body: Emergency bug fix - load button wasn't enabled after selecting local bam/bai or cram/crai.  (same problem occurring after local vcf.gz/tbi file selection).
gene 4.6.1 release: tag_name: gene_4.6.1
body: 1. Speed up response time for large genes (return coding regions only by default)
2. Filter Mosaic files by experiment_id
gene.iobio v4.6 release: tag_name: v.4.6
body: The following new features, enhancements, and bug fixes are addressed in this release:

- Local file not loading samples in Files dialog #731 
- Gene list badge obscures phenolyzer #735
- Numbers too large #753
- Local cram files #597
- Make Call Variants functionality more obvious #754
- Adding an opentargets.org link to the External Links section of the gene information. #746
- Saving 300 plus variants fails #749
- Loading ClinVar track for genes with 1000+ pathogenic variants never finishes #739
- Set AF filter #759
- Warning on gene limit #751
- Indicate if there are no pubmed papers #718
- Indicate if no ClinVar variants were found #740
- Gray out load button if Bam file isn't provided, handle vcf URL vs local vcf differently~ add optional message in bam file text field #616
- Exon with no coverage isn't flagged #564
- Better indication for when no variants are called #765
gene_4.4.2: tag_name: gene_4.4.2
4.4.1: tag_name: gene_4.4.1