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Pulling latest varfish changes from main BIH #1

Merged
merged 116 commits into from
Apr 3, 2023
Merged

Pulling latest varfish changes from main BIH #1

merged 116 commits into from
Apr 3, 2023

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ahujameg
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@ahujameg ahujameg commented Apr 3, 2023

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holtgrewe and others added 30 commits September 6, 2022 14:17
@holtgrewe
Augment StructuralVariant for counts & BNDs (#566)
b02948c 
Closes: #566
Related-Issue: #566
Projected-Results-Impact: require-revalidation
@holtgrewe
Implementing new in-house background for svs (#32)
2593f01 
Closes: #32
Related-Issue: #32
Projected-Results-Impact: require-revalidation
@holtgrewe
Allow excluding cases from in-house database (#579)
6c57a87 
Closes: #579
Related-Issue: #579
Projected-Results-Impact: require-revalidation
@holtgrewe
Adding distinct de novo genotype setting (#562)
972730b 
Closes: #562
Related-Issue: #562
Projected-Results-Impact: require-revalidation
@holtgrewe
Adding section presets for SV filtration (#616)
696c03d 
Closes: #616
Related-Issue: #616
Projected-Results-Impact: require-revalidation
@holtgrewe
Fix bug with G1K freqs in SV filtration (#619)
f89fd8c 
Closes: #619
Related-Issue: #619
Projected-Results-Impact: require-revalidation
@holtgrewe
Displaying disease gene icon also for SVs (#620).
d0e4fe4 
Related-Issue: #620
Closes: #620
Projected-Results-Impact: none
@holtgrewe
Fix gene constraints for RefSeq intergenic vars (#622).
0bab023 
Related-Issue: #622
Closes: #622
Projected-Results-Impact: none
@holtgrewe
Fix import of tads and geneinfo (#625).
5a681cc 
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
@holtgrewe
De novo preset now uses super strict quality (#624)
8056bf5 
Related-Issue: #624
Closes: #624
Projected-Results-Impact: require-revalidation
@holtgrewe
Create single result row even if multiple clinvar entries (#565)
cfba551 
Related-Issue: #565
Closes: #565
Projected-Results-Impact: require-revalidation
@holtgrewe
Fixing clinvar pathogenic filter (#296)
2bd2e73 
Related-Issue: #296
Closes: #296
Projected-Results-Impact: require-revalidation
@holtgrewe
Adding coordinate indices on HelixMtDb and Mitomap (#635)
66be0db 
Related-Issue: #635
Closes: #635
Projected-Results-Impact: none
@holtgrewe
Warning in case of truncated display (#641).
f5662a9 
Related-Issue: #641
Closes: #641
Projected-Results-Impact: none
@dependabot @holtgrewe
Bump shell-quote from 1.7.2 to 1.7.3 in /varfish/vueapp
da5a3ce 
Bumps [shell-quote](https://github.com/substack/node-shell-quote) from 1.7.2 to 1.7.3.
- [Release notes](https://github.com/substack/node-shell-quote/releases)
- [Changelog](https://github.com/substack/node-shell-quote/blob/master/CHANGELOG.md)
- [Commits](https://github.com/substack/node-shell-quote/compare/v1.7.2...1.7.3)

---
updated-dependencies:
- dependency-name: shell-quote
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
@holtgrewe
Switch linting from codacy to default python tools (#639)
73372f3 
Related-Issue: #639
Closes: #639
Projected-Results-Impact: require-revalidation
@holtgrewe
Improving Clinvar record aggregation (#640).
db01542 
Related-Issue: #640
Closes: #640
Projected-Results-Impact: require-revalidation
@holtgrewe
Documenting new Clinvar aggregation (#640).
db8f83f 
Related-Issue: #640
Closes: #640
Projected-Results-Impact: require-revalidation
@holtgrewe
Fixing versions in documentation (#640)
e2215d5 
Related-Issue: #640
Closes: #640
Projected-Results-Impact: none
@holtgrewe
Fixing Docker builds (#660)
60aa6ae 
Related-Issue: #660
Closes: #660
Projected-Results-Impact: none
@stolpeo
Fixed wrong colored WIP result rows (#673) (#674)
8e2fe3a 
Related-Issue: #673
Projected-Results-Impact: none
@holtgrewe
Fixing ClinVar submission XML generation (#677)
006a436 
Closes: #677
Related-Issue: #677
Projected-Results-Impact: none
@holtgrewe
Regular refresh ClinVar individual from Case (#158)
e863a47 
Related-Issue: #158
Projected-Results-Impact: none
@holtgrewe
Fixing ClinVar export editor timing issues (#667, #668).
bbd4687 
Related-Issue: #667
Related-Issue: #668
Closes: #667
Closes: #668
Projected-Results-Impact: none
@holtgrewe
Fixing hemizygous count display in fold-outs (#646)
1665ffb 
Related-Issue: #646
Projected-Results-Impact: none
@holtgrewe
Fixing clinvar submission sex/gender update (#686)
3abad59 
Related-Issue: #686
Projected-Results-Impact: none
@holtgrewe
Fixing issue with phenotype name in Clinvar (#689)
3fd4370 
Related-Issue: #689
Projected-Results-Impact: none
@stolpeo
Initial vue.js implementation for variant filtration (#563) (#695)
91d2a75 
Related-Issue: #563
Projected-Results-Impact: none
@stolpeo
Changing ClinVar link-out to VCV entry instead of coordinates (#693) (#…
22a4f5b 
…706)

Closes: #693
Related-Issue: #693
Projected-Results-Impact: none
@holtgrewe
Adding unit tests for clinvar export Vue app (#692)
e2e2c25 
Closes: #692
Related-Issue: #692
Projected-Results-Impact: none
holtgrewe and others added 28 commits February 9, 2023 13:38
@holtgrewe
build: bumping varfish-server-worker in Dockerfile (#855)
344c6b6
@holtgrewe
fix: genotype criteria quick preset can now be applied (#856)
625cf68 
* fix: genotype criteria quick preset can now be applied

Previously, the setting was not properly set because of issues with the
value wrapper.

* Fixing case SV track in GenomeBrowser
@holtgrewe
feat: adding generic browser track capability and repeat tracks (#857)
38fcb98
@holtgrewe
fix: cnv, genotype criteria and quick presets (#858)
c6d5e96 
* fix: cnv, genotype criteria and quick presets

* fix to tests
@stolpeo
fix: quick presets in vue filter app (#849) (#862)
1e956c9
@holtgrewe
feat: interpret SV breakpoint overlap with segmental duplications and…
a8e233c 
… repeats (#859) (#860)
@holtgrewe
feat: interpret effective/compatible genotype info from worker (#861) (…
2178238 
…#865)
@holtgrewe
fix: make comments and flags work in SV filtration (#867) (#869)
7b1de6c
@holtgrewe
fix: making IGV button in Vue.js SV filtration work (#870)
4f94a24
@holtgrewe
feat: implement expert load/save for genotype criteria (#872) (#875)
87f24b4
@stolpeo
feat: add export for filter results to vue app (#866) (#876)
33755d9
@stolpeo
fix: igv button in smallvariant results filter vue app (#877) (#881)
7737f24
@stolpeo
fix: confusing genomic region genelist in filter vue app (#878, #879) (…
fc5e7cb 
…#882)
@stolpeo
feat, fix: MT link-out from filter results table vue app (#709, #885) (…
5add60f 
…#886)
@stolpeo
feat: bump varfish server worker version to 0.5.0 (887) (#888)
afc4baf
@stolpeo
fix: igv button creates new empty tab (#889) (#894)
98bf9ad
@stolpeo
fix: quick preset dropdown is empty in vue app (#891) (#896)
970edd7
@stolpeo
revert: quick preset dropdown is empty in vue app (#891) (#896)
6bb0302
@stolpeo
fix: quick preset dropdown is empty in vue app (#900) (#901)
bce57c6
@stolpeo
fix: prioriziation with hpo terms not accepting omim terms (#902) (#903)
1ad920b
@holtgrewe
feat: bumping varfish-server-worker (#899) (#904)
a640fea
@stolpeo
fix: prioriziation with hpo terms not accepting omim terms pt2 (#907) (…
aa18371 
…#908)
@stolpeo
fix: comments flags contains a perpetual spinning icon (#893) (#906)
1ec0be4
@holtgrewe
build: switch to Docker BuildKit (#910)
e682116
@holtgrewe
ci: publish Docker image from CI (#912) (#913)
9116468
@holtgrewe
fix: removing dedup/repeat filter for SVs again (#897) (#915)
7ea4f6c
@holtgrewe
docs: fix admin_ingest.rst (#917)
3be1971
@holtgrewe
docs: small fixes to admin ingest (#918)
f3f13bb
@ahujameg ahujameg merged commit 6418176 into ahujameg:main Apr 3, 2023
ahujameg pushed a commit that referenced this pull request Sep 23, 2024
@stolpeo
feat: hemizygous count is not displayed in varfish variant detail (#1… (
066e2f9 
varfish-org#1860)
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3 participants
@ahujameg @holtgrewe @stolpeo