From aa29c89a6662c0b7e7325e43da0522278f3db7c2 Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 25 Apr 2024 11:28:14 +0200 Subject: [PATCH] Fix end coorinates in ClinVar for for indels (#4593) Co-authored-by: Chiara Rasi --- CHANGELOG.md | 1 + scout/server/blueprints/clinvar/controllers.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3eb86b992b..f447613354 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/) - Fix ClinVar form parsing to not include ":" in conditionType.id when condition conditionType.db is Orphanet - Fix condition dropdown and pre-selection on ClinVar form for cases with associated ORPHA diagnoses - Improved visibility of ClinVar form in dark mode +- End coordinates for indels in ClinVar form ## [4.81] ### Added diff --git a/scout/server/blueprints/clinvar/controllers.py b/scout/server/blueprints/clinvar/controllers.py index 443b81b2c0..27cf258216 100644 --- a/scout/server/blueprints/clinvar/controllers.py +++ b/scout/server/blueprints/clinvar/controllers.py @@ -107,7 +107,7 @@ def _get_snv_var_form(variant_obj, case_obj): var_form.variations_ids.data = var_ids.split(";")[0] var_form.chromosome.data = variant_obj.get("chromosome") var_form.start.data = variant_obj.get("position") - var_form.stop.data = variant_obj.get("position") + var_form.stop.data = variant_obj.get("end") return var_form @@ -276,7 +276,7 @@ def parse_variant_form_fields(form): clinvar_var["variations_ids"] = form["dbsnp_id"] if clinvar_var.get("ref_seq") and clinvar_var.get("hgvs"): - # Variant is described by RefSeq and HGVS already, remove redundanti fields from submission + # Variant is described by RefSeq and HGVS already, remove redundant fields from submission for item in ["chromosome", "start", "stop", "ref", "alt"]: clinvar_var.pop(item)