Clinical-Genomics/scout issues and pull requests

#4003 - Add REVEL to the variantS filtering options

Issue - State: closed - Opened by northwestwitch over 1 year ago - 1 comment
Labels: enhancement, Customer Request

#4002 - Export 500 gene variants resulting from SNVs and Indels queries

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 7 comments

#4000 - Support for chanjo2

Issue - State: closed - Opened by northwestwitch over 1 year ago - 19 comments
Labels: enhancement, Intermediate

#3999 - Fix app crashing on Phenopacket import error

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments

#3998 - Include ClinVar variants into a scrollable div on Case page

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 2 comments
Labels: Customer Request, Easy, QualityOfLife, Frontend

#3997 - put a size limit on 'submitted to clinvar' box?

Issue - State: closed - Opened by ielvers over 1 year ago - 2 comments

#3996 - Fix unreferenced canonical_transcript in institute's controllers

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments

#3995 - UnboundLocalError: local variable 'canonical_transcript' referenced before assignment

Issue - State: closed - Opened by northwestwitch over 1 year ago
Labels: bug

#3994 - google.protobuf.json_format.ParseError: Failed to load JSON error

Issue - State: closed - Opened by northwestwitch over 1 year ago
Labels: bug

#3993 - Allow LOMPE long read wgs uploads

Issue - State: open - Opened by dnil over 1 year ago - 1 comment
Labels: enhancement

#3992 - Investigate integrating PubCaseFinder

Issue - State: open - Opened by dnil over 1 year ago - 1 comment
Labels: enhancement, Future ideas

#3991 - New HPO release 230617

Issue - State: closed - Opened by dnil over 1 year ago - 2 comments
Labels: Task

#3990 - Feature request - Upload of RNA bam to WGS cases

Issue - State: closed - Opened by karlnyr over 1 year ago - 4 comments
Labels: enhancement, Customer Request

#3989 - Clearer pop freq in variants list

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments
Labels: Easy, QualityOfLife, Frontend

#3988 - Tornado security issue

Issue - State: closed - Opened by dnil over 1 year ago - 2 comments

#3987 - Fixed column widths on caseS page

Pull Request - State: closed - Opened by dnil over 1 year ago - 2 comments
Labels: Easy, Frontend

#3986 - OMIM-AUTO panel gets saved with yesterday's date

Issue - State: closed - Opened by northwestwitch over 1 year ago - 2 comments

#3985 - Multiselect styles for bootstrap5 dark

Issue - State: closed - Opened by dnil over 1 year ago
Labels: enhancement, QualityOfLife

#3984 - Check the numbers of removed variants by type when the scout delete variants command is involked

Issue - State: open - Opened by northwestwitch over 1 year ago
Labels: Task

#3983 - Button title on "add to submission"

Issue - State: closed - Opened by dnil over 1 year ago - 1 comment

#3982 - Create a dedicated column for gnomAD frequencies in variantS view

Issue - State: closed - Opened by northwestwitch over 1 year ago

#3980 - Add ClinVar API key and allowed submitters to the Institute's settings

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 4 comments

#3979 - Fix assigned name when id is different from email

Pull Request - State: closed - Opened by maehler over 1 year ago - 7 comments

#3978 - New HPO phenotypes release 2023-06-06

Issue - State: closed - Opened by northwestwitch over 1 year ago - 4 comments
Labels: Task

#3977 - Fix gene variant hgvs

Pull Request - State: closed - Opened by dnil over 1 year ago - 3 comments
Labels: Easy

#3976 - Improved Institute Settings layout

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

#3975 - Fix prettylink MEI - fix #3974

Pull Request - State: closed - Opened by dnil over 1 year ago - 2 comments

#3974 - Prettylink MEI - link from pinned variant etc points to structural variant page

Issue - State: closed - Opened by dnil over 1 year ago
Labels: bug

#3973 - ClinVar API added keys (combined issue with preClinVar)

Issue - State: closed - Opened by dnil over 1 year ago - 2 comments
Labels: bug

#3972 - Gene variants view missing region, function annotation, HGVS c.

Issue - State: closed - Opened by dnil over 1 year ago - 2 comments

#3971 - Fix #3970 - IGV locus search fix by giving reference id

Pull Request - State: closed - Opened by dnil over 1 year ago - 3 comments

#3970 - IGV locus search disabled

Issue - State: closed - Opened by dnil over 1 year ago - 2 comments
Labels: bug

#3969 - Version 4.69 release branch

Pull Request - State: closed - Opened by dnil over 1 year ago - 3 comments

#3968 - Force update variants count on case re-upload

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 2 comments

#3967 - Something is off with at least the structural variants total counts

Issue - State: closed - Opened by dnil over 1 year ago - 6 comments
Labels: bug

#3966 - Fix #3883. Fix #3884. Somatic score display and filter.

Pull Request - State: closed - Opened by dnil over 1 year ago - 5 comments

#3965 - FontAwesome resource integrity changed.

Pull Request - State: closed - Opened by dnil over 1 year ago - 1 comment

#3964 - FontAwesome update/integrity check fail

Issue - State: closed - Opened by dnil over 1 year ago
Labels: bug

#3963 - Refactor a couple of complex case related files

Pull Request - State: closed - Opened by dnil over 1 year ago - 5 comments
Labels: QualityOfLife, Refactor

#3962 - explicitly declare and freeze tornado for livereload

Pull Request - State: closed - Opened by dnil over 1 year ago - 4 comments

#3961 - Fix template autoreload

Issue - State: closed - Opened by northwestwitch over 1 year ago - 19 comments
Labels: bug, enhancement, QualityOfLife

#3960 - Fix pypi action

Pull Request - State: closed - Opened by dnil over 1 year ago - 2 comments

#3959 - Skip validation in ClinVar submission via API

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 4 comments

#3955 - Show overlapping SNVs for MEI, add overlapping MEI for SV and SNV

Issue - State: open - Opened by dnil over 1 year ago - 1 comment
Labels: enhancement, Customer Request, Intermediate

#3948 - Scout user meeting 230621 10.30-11.30

Issue - State: closed - Opened by dnil over 1 year ago
Labels: Agenda

#3947 - Remove validation buttons in ClinVar API submission form

Issue - State: closed - Opened by northwestwitch over 1 year ago - 9 comments

#3946 - Improvement of "Search SNVs and Indels" function

Issue - State: open - Opened by fulyataylan over 1 year ago - 2 comments
Labels: enhancement

#3945 - Prepare version 4.68

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 8 comments

#3944 - Temp freeze cyvcf2

Pull Request - State: closed - Opened by dnil over 1 year ago - 1 comment

#3943 - Request: ClinVar API key in institute settings

Issue - State: closed - Opened by ehre over 1 year ago - 9 comments
Labels: enhancement

#3942 - cyvcf2 build

Pull Request - State: closed - Opened by dnil over 1 year ago - 4 comments

#3941 - Separate "safe" and "unsafe" request endpoints

Issue - State: open - Opened by dnil over 1 year ago
Labels: Refactor

#3940 - cyVCF2 0.30.20

Issue - State: closed - Opened by dnil over 1 year ago - 4 comments
Labels: bug

#3939 - Fix #3904 - start a bionano access extension..

Pull Request - State: closed - Opened by dnil over 1 year ago - 11 comments
Labels: enhancement

#3938 - Individual ids in Scout

Issue - State: closed - Opened by dnil over 1 year ago
Labels: enhancement

#3937 - Provisionally solved

Issue - State: closed - Opened by dnil over 1 year ago - 8 comments
Labels: enhancement

#3936 - Save revel key/value when building variant objects

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 13 comments

#3935 - REVEL score not added to variant_obj in build_variant from parsed variants.

Issue - State: closed - Opened by alkc over 1 year ago - 5 comments
Labels: bug

#3934 - Restore rank model versions on causatives/verified pages

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments
Labels: Bugfix

#3933 - Rank model version missing from rank scores on causatives page and exports

Issue - State: closed - Opened by dnil over 1 year ago - 1 comment
Labels: bug

#3932 - For starters, fix action versions

Pull Request - State: closed - Opened by dnil over 1 year ago - 2 comments

#3931 - Docker build failing on pycairo

Issue - State: closed - Opened by dnil over 1 year ago - 3 comments

#3930 - Allow caching panel app panels to disk, in particular for panel app green update

Issue - State: open - Opened by dnil over 1 year ago
Labels: enhancement, QualityOfLife

#3929 - Docker image doesn't compile since today

Issue - State: closed - Opened by northwestwitch over 1 year ago - 1 comment
Labels: bug

#3928 - Add ClinVar submission howto also on case page, Variants submitted to ClinVar

Issue - State: open - Opened by northwestwitch over 1 year ago
Labels: Customer Request

#3927 - Fix #3926 - update igv.js to v2.15.6

Pull Request - State: closed - Opened by dnil over 1 year ago - 10 comments

#3926 - Bugfixes in IGV 2.15.5

Issue - State: closed - Opened by dnil over 1 year ago
Labels: enhancement, Easy

#3925 - Show callers on (SV) variantS list, prep for filter

Issue - State: closed - Opened by dnil over 1 year ago
Labels: enhancement

#3924 - Fix #3923 - default panel on pinned sv report

Pull Request - State: closed - Opened by dnil over 1 year ago - 4 comments

#3923 - Panel default selection from large svs in cancer case report

Issue - State: closed - Opened by dnil over 1 year ago

#3922 - Display if a case has been uploaded using one or more gene panels in the Cases list

Issue - State: closed - Opened by northwestwitch over 1 year ago
Labels: enhancement, Easy

#3921 - Show empty institutes

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments

#3920 - Institutes without cases are not shown on institutes page

Issue - State: closed - Opened by northwestwitch over 1 year ago - 3 comments
Labels: bug

#3919 - Remove freeze on Werkzeug lib

Issue - State: closed - Opened by northwestwitch over 1 year ago - 1 comment
Labels: enhancement, Task

#3918 - RD MEI view

Pull Request - State: closed - Opened by dnil over 1 year ago - 8 comments

#3917 - Freeze werkzeug to version<2.2.3

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments

#3916 - Quote and encoding error

Issue - State: closed - Opened by northwestwitch over 1 year ago - 4 comments
Labels: bug

#3915 - Problems using panel for searching for all cases for institute, when it exists with same name for other institute?

Issue - State: open - Opened by dnil over 1 year ago - 18 comments
Labels: bug

GitHub / Clinical-Genomics/scout issues and pull requests