Small fixes

• Re-introduced gene name(s) in verification email subject
• Better PDF rendering for excluded variants in report
• Problem to access old case when is_default did not exist on a panel

Display overlapping svs

Merge pull request #1044 from Clinical-Genomics/release-4.2.0

Bumps version to 4.2.0

Fix small bug in variant controller

Added

• Download of filtered SVs

Fixed

• Fixed broken download of filtered variants
• Fixed visualization issue in gene panel PDF export
• Fixed bug when updating gene names in variant controller

Display all primary transcripts

Merge pull request #1035 from Clinical-Genomics/release-4.1.3

Bumps version to 4.1.3. Updates CHANGELOG

New panel upload

Added

• Option add/replace when updating a panel via CSV file
• More flexible versioning of the gene panels
• Printing coverage report on the bottom of the pdf case report
• Variant verification option for SVs
• Logs uri without pwd when connecting
• Disease-causing transcripts in case report
• Thicker lines in case report
• Supports HPO search for cases, both terms or if described in synopsis
• Adds sanger information to dashboard

Fixed

• Use db name instead of auth as default for authentication
• Fixes so that reports can be generated even with many variants
• Fixed sanger validation popup to show individual variants queried by user and institute.
• Fixed problem with setting up scout
• Fixes problem when exac file is not available through broad ftp
• Fetch transcripts for correct build in adapter.hgnc_gene

Fix small bugs

• Fix problem with comments
• Fix problem with ensembl link

Panel-app etc

Added

• OMIM phenotypes to case report
• Command to download all panel app gene panels scout load panel --panel-app
• Links to genenames.org and omim on gene page
• Popup on gene at variants page with gene information
• reset sanger status to "Not validated" for pinned variants
• highlight cases with variants to be evaluated by Sanger on the cases page
• option to point to local reference files to the genome viewer pileup.js. Documented in docs.admin-guide.server
• option to export single variants in scout export variants
• option to load a multiqc report together with a case(add line in load config)
• added a view for searching HPO terms. It is accessed from the top left corner menu
• Updates the variants view for cancer variants. Adds a small cancer specific filter for known variants
• Adds hgvs information on cancer variants page
• Adds option to update phenotype groups from CLI

Fixed

• Improved Clinvar to submit variants from different cases. Fixed HPO terms in casedata according to feedback
• Fixed broken link to case page from Sanger modal in cases view
• Now only cases with non empty lists of causative variants are returned in adapter.case(has_causatives=True)
• Can handle Tumor only samples

Fixes upload research

Updates:

• Possible to search for one specific case with case_id in scout view cases
• Display all information for a case in scout view cases

Bugfixes:

• There was a typo in scout load research that accessed vcf_sv_research when looking for cancer vcf
• Tried to access case_id instead of _id in log messages which made the app crash