Merge pull request #19 from artic-network/18-edge-case-with-non-paired-read-with-no-primers

Add check for paired reads

Author: BioWilko

.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

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",

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*"]