From db68c25f867036c2d44f5988863908206a26b969 Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Mon, 30 Sep 2024 07:42:29 +0200 Subject: [PATCH] Small improvements --- CHANGELOG.md | 2 +- src/chanjo2/meta/handle_d4.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d31b56b8..97ffaf09 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ - Updated tests workflow to cargo install the latest d4tools from git (master branch) - Computing coverage completeness stats using d4tools `perc_cov` stat function (much quicker reports) - Moved functions computing the coverage stats to a separate `meta/handle_coverage_stats.py` module -- Refactored gene code computing stats for gene overview +- Refactored code collecting stats shown on gene overview report ### Fixed - Updated dependencies including `certifi` to address dependabot alert - Update pytest to v.7.4.4 to address a `ReDoS` vulnerability diff --git a/src/chanjo2/meta/handle_d4.py b/src/chanjo2/meta/handle_d4.py index fb37d940..4f7043a5 100644 --- a/src/chanjo2/meta/handle_d4.py +++ b/src/chanjo2/meta/handle_d4.py @@ -154,7 +154,7 @@ def get_gene_overview_stats( sql_intervals: List[SQLTranscript], samples: List[ReportQuerySample], completeness_thresholds=List[int], -): +) -> Dict[str, list]: """Returns stats to be included in the gene overview page.""" interval_ids_coords: List[Tuple[str, Tuple[str, int, int]]] = [ (interval.ensembl_id, (interval.chromosome, interval.start, interval.stop))