default CT if empty sailor flag provided

YeoLab · Aug 21, 2024 · f3423c7 · f3423c7
1 parent 2e56ed4
commit f3423c7
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Showing 4 changed files with 237 additions and 1,939 deletions.
diff --git a/marine.py b/marine.py
@@ -572,7 +572,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in
     parser.add_argument('--contigs', type=str, default='all')
     parser.add_argument('--min_read_quality', type=int, default=0, help='Minimum read quality, default is 0... every aligner assigns mapq scores differently, so double-check the range of qualities in your sample before setting this filter')
 
-    parser.add_argument('--sailor', type=str, default=None, dest='sailor')
+    parser.add_argument('--sailor', type=str, nargs='?', const='CT', default=None, dest='sailor')
 
     parser.add_argument('--bedgraphs', type=str, default=None, help='Conversions for which to output a bedgraph for non-single cell runs, e.g. CT, AI')
     parser.add_argument('--verbose', dest='verbose', action='store_true')