Commits

Anton Goloborodko committed d42282c

mapping.py: add code watching for the typo from the publication (--score-min -L)

  • Participants
  • Parent commits c09bc32

Comments (0)

Files changed (1)

File src/hiclib/mapping.py

     nthreads = kwargs.get('nthreads', 4)
     max_reads_per_chunk = kwargs.get('max_reads_per_chunk', -1)
     bowtie_flags = kwargs.get('bowtie_flags', '')
+    # Check for a typo from the publication.
+    assert re.search('--score-min(\s+)-L', bowtie_flags) is None, (
+        'The flag --score-min -L 0.6,0.2 in the original publication was a typo. '
+        'The correct notation is --score-min L ... . Please fix the supplied '
+        'flags.')
+
     temp_dir = os.path.abspath(os.path.expanduser(
         kwargs.get('temp_dir', tempfile.gettempdir())))