Comments (3)
AlistairNWard
commented on September 3, 2024
I'm just going to track genes there are reported problems with in this issue:
HLA-DRB3
SOX5
GALC
MARCHF6
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tonydisera
commented on September 3, 2024
- Regenerated genes.json based on latest version of gene.iobio.db.
- Improved error handling so that user is warned with specific message if gene cannot be annotated because the chromsome is not in the VCF. (example: HLA-DRB3 is on a non standard chr6 chromosome).
- Also improved error handling so that user is warned if we had to switch from Gencode to RefSeq or vice versa for a particular gene because that is the only gene source with transcripts for the particular gene.
- Now an error glyph shows up next to the genes button in the left-side panel gene button.
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AlistairNWard
commented on September 3, 2024
Looks good to me
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Related Issues (20)
- Move ncbi api key to .env that isn't checked into repo
- Use csi as well as tbi indexes HOT 2
- Refine logic for 'poor' and 'moderate' sequence quality on Variant inspect card. HOT 1
- Remove obsolete code for local vcf and bam files
- Remove obsolete code for SFARI
- Real-time / saved data
- For public gene.iobio, user should be able to save analysis and reload later with quick response times.
- Improve error reporting and show errors, warnings, and info as alerts in Notifications sidebar.
- Introduce transcript card
- Create new screencast based on latest UI and functionality introduced in gene 4.7
- Fix intermittent bug where first variant selected after 'analyze all' completed results in empty set of variants in variants card.
- Filtering on variants results in different set of variants when launching saved analysis vs. launching with variant set. HOT 2
- Rename flagged variants heading 'Filtered variants' and 'Not found' to more descriptive terms
- Maintain consistent order of filters in left hand Variants panel
- In the flagged variants panel, sort the variants alphabetically by gene name within a filter
- Since NCBI eutils on gene fails quite often, don't show as 'warning' in app notifications.
- When a problem is encountered in gene coverage, it is preventing variants from being annotated.
- IGH gene has 2 entries in RefSeq gf
- v4.7.1 Side-panel Bugs (progression and variant numbering) HOT 14
- When viewing the list of transcripts, the xref (gencode<->refseq) field is always blank.
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