Ecosyste.ms: Issues

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GitHub / Clinical-Genomics/scout issues and pull requests

#4827 - MIssing cases

Issue - State: open - Opened by sofievonlanthen about 1 month ago - 12 comments
Labels: Clinical Genomics Solna instance only

#4826 - Display WTS outliers again

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 12 comments

#4825 - GT check excludes all variants from the WTS outliers page

Issue - State: closed - Opened by northwestwitch about 1 month ago
Labels: bug

#4824 - Minor release 4.88

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 5 comments

#4823 - Compound top 20 does not show correct order, and shows "not loaded"

Issue - State: closed - Opened by Jakob37 about 1 month ago - 15 comments
Labels: Lund

#4822 - Show SNV/indels in SMN genes on the SMN CN page

Issue - State: open - Opened by Jakob37 about 1 month ago - 2 comments
Labels: enhancement, Under discussion

#4821 - SMN CN page comment field for variant instead of using full case comment field

Issue - State: open - Opened by Jakob37 about 1 month ago - 1 comment
Labels: enhancement, Under discussion, blocked

#4820 - SMN CN page pin button

Issue - State: open - Opened by Jakob37 about 1 month ago - 3 comments
Labels: enhancement, Under discussion

#4819 - test revert igv.js to v2

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 7 comments

#4818 - IGV hangs while loading sample tracks

Issue - State: closed - Opened by northwestwitch about 1 month ago - 4 comments
Labels: bug, wontfix

#4816 - Refactor RNA handling

Issue - State: closed - Opened by dnil about 1 month ago

#4815 - Fix #4814 - actually use variant sample in displaying omics variants

Pull Request - State: closed - Opened by dnil about 1 month ago - 9 comments

#4813 - Patch version 4.87.2

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 3 comments

#4812 - Show CoLoRSdb freq in Pop Freq cell on variantS page

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 3 comments
Labels: Easy

#4811 - Fix coverage upload

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 2 comments

#4810 - design principles, extensions

Issue - State: closed - Opened by parlar about 1 month ago - 4 comments
Labels: question

#4809 - Upload coverage step in GitHub actions seems broken

Issue - State: closed - Opened by northwestwitch about 1 month ago - 6 comments
Labels: bug

#4808 - Selective case update

Issue - State: open - Opened by dnil about 1 month ago
Labels: enhancement, Intermediate, RNA-seq

#4807 - Invalid tag names in VCF: prod & demo

Issue - State: open - Opened by dnil about 1 month ago

#4806 - Fix setup database command

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 4 comments
Labels: Easy, Bugfix

#4803 - Partially fix #4802 - update demo VCF header with missing keys

Pull Request - State: closed - Opened by dnil about 1 month ago - 6 comments

#4802 - setup problems, hgnc_genes

Issue - State: closed - Opened by parlar about 1 month ago - 7 comments
Labels: bug

#4801 - Rename camel case columns

Pull Request - State: closed - Opened by dnil about 1 month ago - 7 comments

#4800 - DROP TSV header - a few more headings camel case

Issue - State: closed - Opened by dnil about 1 month ago

#4799 - Update case omics files

Pull Request - State: open - Opened by dnil about 1 month ago - 4 comments
Labels: enhancement

#4798 - third-party interpretation tool integration

Issue - State: closed - Opened by parlar about 1 month ago - 7 comments
Labels: Under discussion

#4797 - Update case command options for omics_files

Issue - State: open - Opened by dnil about 1 month ago
Labels: enhancement

#4796 - WTS outlier genes flagged on SNV-SV-variantS view

Issue - State: open - Opened by dnil about 1 month ago
Labels: enhancement, QualityOfLife, RNA-seq

#4794 - Colorsdb on variantS pop freq tooltip?

Issue - State: closed - Opened by dnil about 1 month ago
Labels: enhancement, QualityOfLife, LRS

#4793 - Patch 4.87.1 - fix genes cell on variantS page

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 3 comments

#4792 - Ugliness on variantS list: multiple gene names get squished together, and overflow to nearby column

Issue - State: closed - Opened by dnil about 1 month ago - 8 comments
Labels: bug

#4791 - Fix #4790 - trailing comma

Pull Request - State: closed - Opened by dnil about 1 month ago - 2 comments

#4789 - Coloring alignments by base modification removes read grouping

Issue - State: open - Opened by fellen31 about 1 month ago - 9 comments
Labels: enhancement, QualityOfLife, blocked

#4788 - Show genes track also when RNA alignments are present without splice junctions tracks

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 2 comments

#4787 - Unscrollable splice junctions track

Issue - State: closed - Opened by northwestwitch about 1 month ago - 6 comments

#4786 - Update igv.js to 3.0.4.

Pull Request - State: closed - Opened by dnil about 1 month ago - 3 comments
Labels: enhancement, Easy

#4785 - Version 4.87 - configure RNA build, add igv.js genome aliases

Pull Request - State: closed - Opened by dnil about 1 month ago - 11 comments

#4784 - Fix #4782 - explicit igv.js chr alias option

Pull Request - State: closed - Opened by dnil about 1 month ago - 2 comments
Labels: Easy, Bugfix

#4783 - Fix #4782 - IGV does not remove chr str from non-autosomes

Pull Request - State: closed - Opened by dnil about 1 month ago - 8 comments
Labels: Bugfix

#4782 - Issues to access IGV from variant page

Issue - State: closed - Opened by sofievonlanthen about 1 month ago - 4 comments

#4781 - Fix #4780 - RNA aln genome build tooltips

Pull Request - State: closed - Opened by dnil about 1 month ago - 3 comments

#4780 - Change only in hg38 RNA tooltip

Issue - State: closed - Opened by dnil about 1 month ago
Labels: enhancement, QualityOfLife

#4779 - Fix style of SNVs and SVs buttons on WTS Outliers page

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 2 comments
Labels: Easy, Frontend

#4778 - Patch release v.4.86.1

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 3 comments

#4777 - Fix panelapp updating error

Pull Request - State: closed - Opened by northwestwitch about 1 month ago - 4 comments
Labels: Easy, Bugfix

#4776 - Missing key error when updating PanelApp green Panel

Issue - State: closed - Opened by northwestwitch about 1 month ago - 1 comment
Labels: bug

#4775 - Fix #4773 - separate RNA view genome build option

Pull Request - State: closed - Opened by dnil about 2 months ago - 2 comments

#4774 - Respect igv tracks settings

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 3 comments

#4773 - RNA view hg19 aln

Issue - State: closed - Opened by dnil about 2 months ago - 1 comment
Labels: enhancement, RNA-seq, Research

#4772 - Fix #4769 - users can disable gene track and still see sashimi view

Pull Request - State: closed - Opened by dnil about 2 months ago - 3 comments

#4771 - OMICS variant SNV, SV button center column alignment

Issue - State: closed - Opened by dnil about 2 months ago
Labels: enhancement, QualityOfLife, Frontend

#4770 - Settings DNA does not respect disabling certain tracks.

Issue - State: closed - Opened by dnil about 2 months ago - 1 comment
Labels: bug

#4769 - Splice junction track needs gene track enabled, otw does not show junctions.

Issue - State: closed - Opened by dnil about 2 months ago - 2 comments
Labels: bug

#4768 - Fix #4764 - timestamp activity

Pull Request - State: closed - Opened by dnil about 2 months ago - 3 comments

#4767 - Show time (hours and minutes) additionally to date on comments and activity panel

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 5 comments
Labels: Easy, QualityOfLife

#4766 - Re-style case HPO terms to have one phenotype per line

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 10 comments
Labels: Customer Request, Easy

#4765 - Don't linebreak between phenotype checkbox and label. Add select all phenotypes button.

Issue - State: closed - Opened by dnil about 2 months ago - 2 comments
Labels: enhancement, Customer Request

#4764 - Show hh:mm timestamp on activity log

Issue - State: closed - Opened by dnil about 2 months ago
Labels: QualityOfLife

#4763 - Expand institute view to include stats on type of cases

Issue - State: open - Opened by northwestwitch about 2 months ago
Labels: enhancement, QualityOfLife

#4762 - Switch to non-kit FontAwesome 6

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 3 comments

#4761 - Revert table style and remove font awesome from IGV template

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 2 comments

#4760 - One more attempt at improving legibility of gene symbol flash messages

Issue - State: open - Opened by dnil about 2 months ago
Labels: Customer Request, Intermediate, QualityOfLife

#4759 - FontAwesome bundle incorrect again

Issue - State: closed - Opened by dnil about 2 months ago

#4758 - Add user sending requests to log

Issue - State: open - Opened by Vince-janv about 2 months ago
Labels: enhancement

#4757 - Connectivity to gene matcher seems limited atm?

Issue - State: open - Opened by dnil about 2 months ago - 2 comments
Labels: bug

#4756 - Update flash message for MatchMaker to reflect new modal

Issue - State: open - Opened by dnil about 2 months ago
Labels: enhancement, Easy

#4755 - Error sending data to patientMatcher

Issue - State: closed - Opened by northwestwitch about 2 months ago - 1 comment

#4754 - Download -omics variants

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 2 comments

#4753 - Add more IGV tracks to the splice junctions browser?

Issue - State: open - Opened by northwestwitch about 2 months ago
Labels: enhancement, Under discussion

#4752 - Minor version 4.86

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 11 comments

#4751 - Update tornado to address open redirect security issue

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 3 comments
Labels: Easy

#4750 - New HPO release 2024-08-13

Issue - State: closed - Opened by northwestwitch about 2 months ago - 3 comments
Labels: Task, blocked

#4749 - Fix ExAC links

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 2 comments
Labels: Easy, Bugfix

#4748 - Links to ExAC are no longer valid

Issue - State: closed - Opened by northwestwitch about 2 months ago
Labels: bug

#4747 - Parse and show CoLoRSdb frequencies

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 4 comments
Labels: Easy

#4746 - Parse gnomad keys from variants annotated with echtvar

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 3 comments
Labels: Easy

#4745 - Load less mei variants in scout demo instance

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 3 comments
Labels: Easy, QualityOfLife

#4744 - Case tags dashboard

Pull Request - State: closed - Opened by dnil about 2 months ago - 3 comments

#4743 - Dashboard stats for case tags

Issue - State: closed - Opened by dnil about 2 months ago
Labels: enhancement

#4742 - Add CoLoRSdb and gnomAD keys

Issue - State: closed - Opened by fellen31 about 2 months ago - 9 comments
Labels: enhancement, LRS

#4741 - Update Chart.js to v4.4.3

Pull Request - State: closed - Opened by dnil about 2 months ago - 4 comments

#4740 - UpdateChart.js

Issue - State: closed - Opened by dnil about 2 months ago - 1 comment

#4739 - Fix #4738 - IGV sashimi routing hint

Pull Request - State: closed - Opened by dnil about 2 months ago - 2 comments

#4738 - IGV RNA junction track variant locus zoom not working

Issue - State: closed - Opened by dnil about 2 months ago
Labels: bug

#4737 - Occasional crashes when testing IGV junction tracks

Issue - State: closed - Opened by dnil about 2 months ago
Labels: bug

#4736 - Update wokeignore to avoid unfixable warning

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 2 comments
Labels: Easy, QualityOfLife

#4735 - Fix #4734 - spliceJunction height offset

Pull Request - State: closed - Opened by dnil about 2 months ago - 2 comments

#4734 - Height offsets for merged RNA tracks with IGV 3.0.1

Issue - State: closed - Opened by dnil about 2 months ago
Labels: bug

#4733 - Clickable COSMIC IGV tracks

Pull Request - State: closed - Opened by northwestwitch about 2 months ago - 5 comments
Labels: enhancement, QualityOfLife

#4732 - MEI loading is slow in tests

Issue - State: closed - Opened by dnil 2 months ago
Labels: QualityOfLife, Refactor

#4731 - Fix #4729 - check caller keys also from FOUND_IN and SVDB_ORIGIN before adding

Pull Request - State: closed - Opened by dnil 2 months ago - 2 comments

#4730 - Sort IGV tracks - fix #4726

Pull Request - State: closed - Opened by dnil 2 months ago - 2 comments
Labels: Easy, Frontend

#4729 - Nonsensical key/value in demo instance variant

Issue - State: closed - Opened by northwestwitch 2 months ago - 7 comments
Labels: bug

#4728 - Make IGV tracks's items clickable

Issue - State: closed - Opened by northwestwitch 2 months ago - 1 comment
Labels: enhancement, Frontend

#4727 - Audit buttons for pages without filters

Issue - State: open - Opened by dnil 2 months ago
Labels: enhancement, QualityOfLife

#4726 - Sort selectable IGV tracks alphabetically

Issue - State: closed - Opened by northwestwitch 2 months ago
Labels: Easy, Frontend

#4724 - Update igv.js to v 3.0.1

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 8 comments
Labels: Easy