Skip to content

Improved pagination, SV page and paraphase view, added variantS keyboard shortcuts, and much more

Choose a tag to compare

View all tags
@dnil dnil released this 15 Oct 10:17
· 275 commits to main since this release
v4.105.1
9d0fe8c
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

Scout version 4.105.1

There was no official 4.105 release, due to an old uv.lock file.

ADMINS - Please note that this release has a (non essential) database index update for the hgnc genes part of the database. If your db is small enough, simply drop indices and rebuild them. Otherwise, run
scout index --update -c hgnc_gene and manually remove the old indices in that collection (all starting with build, leaving only the new build_chromosome_start_end with that prefix).

See PR #5532 for details on updating to chanjo2 with authentication. Essentially, if you enable authentication, also upgrade your chanjo2 service to version 3.9.

We introduce a typo corrected --rank-threshold option alias for the already deprecated one (#5720). If you use this in your workflows, consider if it is a good time to change it. The fallback is scheduled for removal with Scout v5.

For the web user interface, we have introduced some keyboard shortcuts for the variantS pages. Try them out and let us know if they work for you, if you want more or different ones! Excerpt from the updated user guide:

Hotkeys available on all variantS pages

Some variants hotkeys are sensitive to which row you are currently hovering over.

  • d for checking Dismiss checkbox on current row
  • v for opening a Variant on current row (open the variant, typically in a new _blank tab)

Others give you quick access to a given function.

  • c Clinical filter
  • f Filter variants
  • g focus input on the Gene symbol field, un-collapsing filter if needed
  • b toggle dismiss Bar

[4.105.1]

Fixed

  • uv lockfile update (#5780)

[4.105]

Added

  • Support for variants annotated with an unmodified ClinVar VCF (#5691)
  • Parse and display copy number on SV page, genotype table (#5692)
  • Bootstrap-based pagination on variantS pages (#5697)
  • More transcript insights on variant summary for SV variants hitting max 5 genes (#5706)
  • Button to export ACMG classifications to PDF (#5715)
  • CLINSIG table on SV variant page (#5718)
  • Search genes at breakpoint for larger SVs (#5722)
  • Code for refreshing id token, if needed. To be used for authenticated requests to chanjo2 (#5532)
  • Genotypes on Search SNVs & SVs page (#5737)
  • Display the number of fusion variants on the variantS page, just like the other variant types (#5754)
  • Keyboard shortcuts on the variantS pages - see the updated user guide for details (#5768)

Changed

  • Better access to ALT allele for SVs (#5694)
  • Remove unused variant_count parameter from several functions involved with variant queries (#5700)
  • Consolidated and simplified case handling tests (#5708)
  • Authorize access to IGV.js track files at endpoint, instead of by session cookie. Allows huge case groups and many open IGV.js sessions. (#5712)
  • On the variant page, the corresponding button opens the ACMG and CCV classification tools in a new tab (#5723)
  • Fix CLI parameter typo --rank-treshold with backward-compatible alias and deprecation warning (#5720)
  • Safer redirect to previous page for all views and controllers still using redirect(request.referrer)(#5721)
  • Default paraphase igv.js track settings: color by YC, squish, extend visibility window, auto-height and place last in view. (#5724)
  • Chanjo2 requests are sent with OIDC id token, if available (#5532)
  • Refactored and simplified SV, cancer SV and MEI variants views (#5701)
  • Replaced deprecated flask-ldapconn library with flask-ldap3-login. Modified LDAP login module accordingly (#5719)
  • Update IGV.js to v3.5.3 (#5757)
  • Specify in the MT report that Chanjo2 stats are based on full chromosomes MT and 14, not transcript intervals. (#5771)

Fixed

  • Typo in PR template (#5682)
  • Highlight affected individuals/samples on GT call tables (#5683)
  • Refactored and simplified the LoqusDB archived observations table. -1 is no longer shown for missing observations (#5680)
  • Fix a parsing issue with VEP annotations done with --check_existing where the CSQ key CLIN_SIG would be prioritised over CLINVAR (#5691)
  • Display variant rank score 0 (#5699)
  • Show only IGV link to breakpoint1 for SVs of sub-category INS (#5694)
  • Allow updating case owner on scout load case -u (#5681)
  • Missing query results on STR variantS page (#5713)
  • Links to variants with missing rank scores from Causatives and Verified pages (#5715)
  • Clinical filter button on research variants, wrongly redirecting to respective clinical variants pages (#5725)
  • Pagination to handle empty search results (#5727)
  • Gene variants page to return all resulting variants again (#5727)
  • Gene panel parsing if gene doesn't contain an identifier (#5733)
  • Include both chanjo and chanjo2 stats on MT report (#5686)
  • Institute cases filtering with Has ClinVar submissions checkbox (#5735)
  • Display plain variant rank score also if norm rank score is missing (#5738)
  • Missing cairo runtime dependency (#5750)
  • Fix pagination for somatic SVs (#5746)
  • Fix display of STR MC for cases with GT "./0" calls (#5749)
  • Build full HGNC genes for STR variants with HGNCId on load (#5751)
  • Use proper end position for large SVs when looking up edge genes (#5755)
  • Fixed crash on the Gene Panel page when changes to the same panel version were applied from multiple browser tabs (#5762 and #5765)
  • Sort STRs primarily by HGNC symbol, if available (#5763)
  • Refresh login token on stale case pages before submitting chanjo2 forms (#5772)
  • Safer code in gene panel parsing (#5778)
Assets 2
Loading