Renamed counts to Counts(germline only) on overlaps page #1046
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TheMadBug
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* Panal App VUS/GUS relationship download * Panal App VUS/GUS relationship download * Providing methods to find more useful relationships between term and gene symbol for report * issue #2647 - liftover refactor * issue #2647 - start of bcftools liftover * Issue #2647 - BCFTools liftover * Issue #2647 - Remove vestigial NCBI remap traces * Issue #2647 - enable in vg test * Stop warning that doesn't apply here * Issue #2647 - be able to create variant for long ones... * This occasionally failed - execution continued after asking to change window * issue #1054 - make bcftools liftover part of standard ANNOTATION settings * issue #1054 - misc liftover issues * Issue #1052 - analysis template version * Make VEP have version in path * Shariant test config - enable BCFTools liftover * Upload initially shows error wrongly in pipeline race condition * issue #818 - don't uniq on preprocess anymore * issue #1056 - vcf_clean_and_filter convert contig headers * issue #1057 - VEP deployment change to explicit version * vg test config * issue #980 - karyomapping use symbol instead of gene * Renamed counts to Counts(germline only) on overlaps page (#1046) * Fix issue where alleleOriginToggle was being called with undefined * WIP fixing conda dependencies * Update of conda environment (works again in conda) * Add new evidence key for somatic testing * Show better quick clinical significance values (for somatic and germline) * Fix recently introduced bug in suggested terms for an allele * Allow link for condition matching to appear on a classification even when not in edit mode * issue #1059 - all variants node * issue #1059 - all variants node * Adjust node counts a little * issue #1043 - export VCF * Tidy up server status page removing redundant data (now go to Overall Status) * Fix the evidence key values * Get c.HGVS showing properly on variant details page again * issue #758 - configure quick links via settings * More comments in conda file * Move condition text match from classification.html to JSON to keep things in sync More requirements on when you will be linked to condition resolution * Style fixes for new liftover * Put liftover date on form * Move overall data to the splash server status page * Add Clinical Trails gov to quick links * Add liftover to settings menu if variants menu disabled * Update shariant prod settings to use VEP v108 * Make liftover page side menu change based on settings * Better wording for changing clinical contexts within a discordance * Tighten up the handling of embedded card or modal (used for triage but affected other modals by mistake) * Better safety around condition text relationships * For view metrics use heading of "Users" not "User" * Add overall stats to liftover pages * Slight formatting on liftover note * Rework the internals of the view user activity reports * More styling on liftover runs page * More styling on liftover pages * Tiny column alignment issue on liftover * linting * Fix exclusion of blank searches in metrics * Subtle change of header wording for activity report * Improve the formatting of missing IDs when making a batch for ClinVar * Proper int to string handling for missing IDs * issue #758 - quick links via settings * Reworking of Lab Differences using new zippable functionality for ExportRow * Put the allele URL into the lab compare (I think it was there before) * Enable SEARCH_HGVS_GENE_SYMBOL_USE_MANE for shariant test * Also try enabling SEARCH_HGVS_GENE_SYMBOL * Fix bug where condition URL was calculated before seeing if we had condition text * Enable extra variant annotations for testing * Attempt at parsing OncogenicityClassification for pulling in ClinVar records * issue #1193 - analysis audit log * issue #1193 - analysis audit log * issue #1193 - analysis audit log * issue #1193 - analysis audit log * issue #1193 - analysis audit log * variantgrid_private#1193 - Audit log for analysis * Get audit log name right in requirements * issue #1060 - variant details page, create allele for all variants not just shorty clingen ones * Sometimes can't reload analysis #1061 * issue #1193 - disable audit log for template copies etc * issue #1193 - Audit log for analysis - click to expand and see JSON * issue #1193 - Don't audit node cloning (was causing tests to fail) * temp fix for #1053 - will work out data fix later * Better categorising of ClinVar's Somatic/Germline records * issue #1053 - cohort genotype versions - make common cohort version match cohort.version * linting - format whitespace * linting - remove unused imports * Unused file * linting - f string w/o interpolation * linting - use generator * Increase the ClinVar parser version to purge old cache * Add django-audit-log to conda environment * ClinVar REcords More work on parsing condition * issue #1053 - missing import, make sure we retrieve only 1 cgc per cohort * issue #877 - Export column - c_hgvs_compat * Add MeSH as a non-local ontology set * Ability to render multiple conditions against a single ClinVar record * Don't abbreviate ref/alt in VCF * Fix bug with filtering out non-human clinvar records * Count homo sapiens, homo-sapiens, homosapiens the same as human for ClinVar records * A script to close manually raised flags * Raise classification change flag for both Classification and Somatic Clinical Significance * Filter based on creator of flag * Added prefixed clinvar batch export CB_ and clinvar export CE_ search functionality (#1066) * issue #3604 - COSMIC search * Update changelog * Tidy up code for close flags, allow it to re-open flags * Bug fixes for the condition checking code * panalapp work * PanelApp Compare: Fixes to stop infinite recurssion, correct method signatures. * #3591 panel app export --------- Co-authored-by: TheMadBug <[email protected]> Co-authored-by: Dave Lawrence <[email protected]>
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