Clinical-Genomics/scout issues and pull requests

#4621 - Clearer warning for sample sex mismatch

Issue - State: closed - Opened by Jakob37 5 months ago - 1 comment
Labels: Customer Request, QualityOfLife

#4620 - Revert installation of flask-ldapconn

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 6 comments
Labels: Bugfix

#4619 - Change LDAP library?

Issue - State: closed - Opened by northwestwitch 5 months ago - 1 comment
Labels: Under discussion

#4618 - Freeze werkzeug again

Pull Request - State: closed - Opened by dnil 5 months ago - 3 comments

#4617 - debug Alchy load and route...

Pull Request - State: closed - Opened by dnil 5 months ago - 3 comments

#4616 - '_bcf_float_missing' error executing scout from local installation

Issue - State: closed - Opened by northwestwitch 5 months ago - 5 comments
Labels: duplicate

#4615 - Fix installation of libraries in second build stage of Dockerfile

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 2 comments

#4614 - No chanjo-report endpoint found

Issue - State: closed - Opened by northwestwitch 5 months ago - 2 comments
Labels: bug

#4613 - Revert to primary flask-ldapconn once its PyPi is up to date

Issue - State: closed - Opened by dnil 5 months ago - 2 comments
Labels: Easy, Refactor, blocked

#4612 - Unfreeze werkzeug

Pull Request - State: closed - Opened by dnil 5 months ago - 4 comments

#4611 - Prod/stage divide for CLINVAR settings

Issue - State: closed - Opened by dnil 5 months ago
Labels: enhancement

#4610 - Werkzeug vuln <3.0.3

Issue - State: closed - Opened by dnil 5 months ago - 2 comments

#4609 - ncRNA genes and the clinical filter

Issue - State: open - Opened by ielvers 5 months ago - 9 comments
Labels: enhancement, Under discussion

#4608 - Fix case crashing when evaluating ClinVar vars among pinned not loaded variants

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

#4607 - Error adding variant to ClinVar

Issue - State: closed - Opened by northwestwitch 5 months ago - 1 comment
Labels: bug

#4606 - Avoid chanjo2 queries when there are no genes available for stats

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 7 comments
Labels: Easy, QualityOfLife

#4605 - User friendly error message for no default panel

Issue - State: closed - Opened by Jakob37 5 months ago - 2 comments
Labels: enhancement, Easy

#4604 - Shall we parse and add to DB obsolete HPO terms?

Issue - State: closed - Opened by northwestwitch 5 months ago - 4 comments
Labels: Under discussion

#4603 - Prepare minor version 4.82

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 14 comments

#4602 - Fix diagnoses API search crashing with empty search string

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 6 comments
Labels: Easy, Bugfix

#4601 - Empty API diagnoses query crashes

Issue - State: closed - Opened by dnil 5 months ago - 1 comment
Labels: bug

#4600 - Use latest gene panel for panel overlap in variantS, variant view and case report

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 4 comments
Labels: Bugfix

#4599 - Use latest gene panel for panel overlap in variantS, variant view and case report

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 2 comments
Labels: Bugfix

#4598 - Display errors loading managed variants from file on relative web page

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 6 comments
Labels: enhancement, Easy

#4597 - Flag coverage dropouts induced by repeat expansions in long-read data

Issue - State: open - Opened by fellen31 5 months ago - 1 comment
Labels: enhancement, LRS

#4596 - "Classify-link" on the Clinical Structural variants-variant page

Issue - State: open - Opened by SofieCMD 5 months ago - 2 comments
Labels: enhancement, Customer Request, Intermediate

#4595 - ClinVar submission status button

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

#4594 - Stricter control over ClinVar condition IDs provided in ClinVar form

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

#4593 - Fix end coordinates in ClinVar for indels

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 3 comments
Labels: Easy, Bugfix

#4592 - Typehead diseases when query contains source substring

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

#4591 - Fix ORPHA dropdown and preselected diagnoses on ClinVar form

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

#4590 - ClinVar submission error - variant location for indel

Issue - State: closed - Opened by dnil 5 months ago - 1 comment
Labels: bug

#4589 - Fix ClinVar form parsing to not include : in conditionType.id when condition is Orphanet

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

#4588 - Autocompletion on case page diagnosis field to include entry number

Issue - State: closed - Opened by dnil 5 months ago
Labels: QualityOfLife

#4587 - Fix installation of wkhtmltopdf in GitHub action

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 2 comments
Labels: Bugfix

#4586 - ClinVar submission Orphanet db tag gets inserted with colon..

Issue - State: closed - Opened by dnil 5 months ago - 2 comments
Labels: bug

#4584 - Test action fails when installing the PDF renderer

Issue - State: closed - Opened by northwestwitch 5 months ago - 4 comments
Labels: bug

#4583 - Improved visibility of ClinVar form in dark mode

Pull Request - State: closed - Opened by northwestwitch 5 months ago - 4 comments
Labels: Easy, Bugfix, Frontend

#4582 - ClinVar submission Associated Conditions Orphanet not pre-selected

Issue - State: closed - Opened by dnil 5 months ago
Labels: QualityOfLife

#4581 - ClinVar submission manual entry field checks

Issue - State: closed - Opened by dnil 5 months ago
Labels: enhancement

#4580 - ClinVar submission dark mode

Issue - State: closed - Opened by dnil 5 months ago - 1 comment
Labels: QualityOfLife

#4578 - Filter cancer variants by old local germline and old local somatic observations

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 4 comments

#4577 - Fix #4445 - load separate MT VCFs

Pull Request - State: closed - Opened by dnil 6 months ago - 9 comments

#4576 - Block ClinVar submission of somatic variants, to reflect changes in ClinVar API

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 2 comments
Labels: Easy

#4575 - Fix link name on caseS page

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 2 comments
Labels: Easy, Bugfix

#4574 - Pagination and nr HPO terms on Phenotypes page

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 4 comments
Labels: enhancement, Easy, QualityOfLife

#4573 - Chanjo2 integration howto

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 2 comments
Labels: docs

#4572 - obophenotype/human-phenotype-ontology release - 2024-04-26

Issue - State: closed - Opened by northwestwitch 6 months ago - 5 comments
Labels: Task

#4571 - Improve PDF view of the delivery reports

Issue - State: closed - Opened by ivadym 6 months ago - 5 comments
Labels: enhancement

#4570 - Fix #4568 - add a STR details panel to the variant page

Pull Request - State: closed - Opened by dnil 6 months ago - 2 comments

#4569 - Changed case report to display more info for fusion variants

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 2 comments
Labels: Customer Request, Easy

#4568 - Gnomad v4 link not working for STR variants

Issue - State: closed - Opened by Jakob37 6 months ago - 5 comments
Labels: bug

#4567 - Fusion variant display on pinned summary table for cancer general reports

Issue - State: closed - Opened by dnil 6 months ago
Labels: enhancement, Customer Request

#4566 - Fix #4469 - parse TRGT STR VCF

Pull Request - State: closed - Opened by dnil 6 months ago - 6 comments

#4565 - Genes exclusion filter criterion

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments
Labels: enhancement, Customer Request, Easy

#4564 - Gene symbols file in variants filter doesn't work

Issue - State: closed - Opened by northwestwitch 6 months ago - 2 comments
Labels: bug

#4563 - Change PDF custom report to portrait view

Pull Request - State: closed - Opened by ivadym 6 months ago - 5 comments

#4562 - Added tooltip for combined compound score

Pull Request - State: closed - Opened by TereseBo 6 months ago - 4 comments

#4561 - Bump IGV version

Pull Request - State: closed - Opened by dnil 6 months ago - 5 comments

#4560 - Add a tooltip on variant's page, compounds table to explain Combined score

Issue - State: closed - Opened by northwestwitch 6 months ago

#4559 - Harmonization of case report spacing for some lists and #panel_tabels

Pull Request - State: closed - Opened by TereseBo 6 months ago - 3 comments

#4558 - On phenotypes page, display number of available phenotypes in the database

Issue - State: closed - Opened by northwestwitch 6 months ago
Labels: Easy, Frontend

#4557 - Optionally adjusting reported coverage limits

Issue - State: open - Opened by Jakob37 6 months ago - 2 comments
Labels: enhancement

#4556 - Minor release 4.81

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 6 comments

#4555 - Fix cancer_rank_options typo in case report

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments
Labels: Easy, Bugfix

#4554 - jinja2.exceptions.UndefinedError: 'cancer_rank_options' is undefined

Issue - State: closed - Opened by northwestwitch 6 months ago - 2 comments
Labels: bug

#4553 - Direct links to chanjo2 external app

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 6 comments
Labels: enhancement, Bugfix

#4552 - Updated inline styling of comment accordion to utilise bootstrap vars

Pull Request - State: closed - Opened by TereseBo 6 months ago - 3 comments

#4551 - Text claiming all pinned variants are represented in causatives is now only rendered if this is true

Pull Request - State: closed - Opened by TereseBo 6 months ago - 3 comments

#4550 - Missing indices..

Issue - State: closed - Opened by dnil 6 months ago - 1 comment
Labels: Task

#4549 - Remove of table data (without header) for inheritance in case_report if cancer case

Pull Request - State: closed - Opened by TereseBo 6 months ago - 3 comments

#4548 - IGV issue with colouring on TLEN / insert size & orientation

Issue - State: open - Opened by dnil 6 months ago - 5 comments
Labels: bug

#4547 - case_report renders wrong text for contents

Issue - State: closed - Opened by TereseBo 6 months ago
Labels: bug

#4546 - Misalignment of headers and table contents in case_report

Issue - State: closed - Opened by TereseBo 6 months ago - 1 comment
Labels: bug

#4545 - Update case_report and panel_reports to use bootstrap 5

Pull Request - State: closed - Opened by TereseBo 6 months ago - 5 comments

#4544 - [obophenotype/human-phenotype-ontology] Release v2024-04-03 - 2024-04-03 Release

Issue - State: closed - Opened by dnil 6 months ago - 4 comments
Labels: Task

#4543 - Add a "missing data" limit constant

Issue - State: open - Opened by dnil 6 months ago
Labels: QualityOfLife, Refactor

#4542 - Fix #4541 - DUX4::IGH BALSAMIC SV caller tag

Pull Request - State: closed - Opened by dnil 6 months ago - 3 comments
Labels: Easy

#4541 - Add igh_dux4 as a caller type for cancer

Issue - State: closed - Opened by fevac 6 months ago - 4 comments
Labels: Easy

#4540 - Directly redirect to chanjo2 when creating reports

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 2 comments

#4539 - Trouble getting /report calls going to the correct end point

Issue - State: closed - Opened by Jakob37 6 months ago - 19 comments
Labels: bug

#4538 - reintroduce and slightly modify variant rankscore sort index

Pull Request - State: closed - Opened by dnil 6 months ago - 6 comments

#4537 - Patch release 4.80.1

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 4 comments

#4536 - Fix button size on HPO panel

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 3 comments
Labels: Easy, Frontend

#4535 - Fix size of buttons on HPO panel

Issue - State: closed - Opened by northwestwitch 6 months ago

#4534 - Link to chanjo2 genes overview on gene panel page

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 5 comments
Labels: enhancement, Easy

#4533 - Sort exceeded memory when loading a case

Issue - State: closed - Opened by northwestwitch 6 months ago - 10 comments

#4532 - Dark mode for comments container

Issue - State: closed - Opened by dnil 6 months ago
Labels: QualityOfLife, Frontend

#4531 - Release v4.80

Pull Request - State: closed - Opened by dnil 6 months ago - 7 comments

#4530 - Fix #4507 - fusion specific fields in export

Pull Request - State: closed - Opened by dnil 6 months ago - 2 comments

#4529 - Add link to genes coverage overview on case page, HPO panel

Pull Request - State: closed - Opened by northwestwitch 6 months ago - 18 comments

#4528 - Panel-table on case-page initially renders default panel in first row

Pull Request - State: closed - Opened by TereseBo 6 months ago - 4 comments

#4527 - Throwing out users???

Issue - State: closed - Opened by KickiLagerstedt 6 months ago - 4 comments

#4526 - Make default panels easier to access / overview

Issue - State: closed - Opened by Jakob37 6 months ago - 1 comment
Labels: Customer Request, QualityOfLife

#4524 - Add a new 'Explanation for multiple conditions` field in ClinVar form when a variant has more that one condition ID

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 3 comments

GitHub / Clinical-Genomics/scout issues and pull requests