From e559d518b2991153d48c3e22c0a8bc65648bd1ed Mon Sep 17 00:00:00 2001 From: ChrisKent Date: Thu, 28 Aug 2025 15:58:47 +0100 Subject: [PATCH 1/3] Add check for paired reads --- align_trim/main.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/align_trim/main.py b/align_trim/main.py index 8a4d8f9..66be3bf 100644 --- a/align_trim/main.py +++ b/align_trim/main.py @@ -372,7 +372,8 @@ def handle_segments( ) if not p1 or not p2: - segment = segment1 if segment1 else segment2 + if paired: + segment = segment1 if segment1 else segment2 if args.verbose: print( f"{segment.query_name}: skipped as no primer found for segment", From b0319ff452d2dad7838fda6325da5dbae686183e Mon Sep 17 00:00:00 2001 From: Sam W Date: Thu, 28 Aug 2025 16:37:00 +0100 Subject: [PATCH 2/3] Bump version from 1.0.1 to 1.0.2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a059400..1a98aa1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "align_trim" -version = "1.0.1" +version = "1.0.2" license = "MIT" license-files = ["LICEN[CS]E*"] From 19bb6eb0e75657b7fe06eca2bd253df429edc7d9 Mon Sep 17 00:00:00 2001 From: Biowilko Date: Thu, 28 Aug 2025 16:40:33 +0100 Subject: [PATCH 3/3] Update uv lock --- .gitignore | 1 + uv.lock | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index cb0f8dc..5c33310 100644 --- a/.gitignore +++ b/.gitignore @@ -25,6 +25,7 @@ share/python-wheels/ .installed.cfg *.egg MANIFEST +.DS_store # PyInstaller # Usually these files are written by a python script from a template diff --git a/uv.lock b/uv.lock index 7b0a2af..3218254 100644 --- a/uv.lock +++ b/uv.lock @@ -9,7 +9,7 @@ resolution-markers = [ [[package]] name = "align-trim" -version = "1.0.1" +version = "1.0.2" source = { editable = "." } dependencies = [ { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },