Contig stitcher: do not require logging=debug for the visualizer

Author: Donaim

micall/core/contig_stitcher.py

@@ -723,10 +723,6 @@ def main(args):
         logger.setLevel(logging.WARN)
 
     logging.basicConfig(level=logger.level)
-    if args.plot and logger.level > logging.DEBUG:
-        logging.error("Option --plot requires --debug.")
-        exit(1)
-
     write_contig_refs(args.contigs.name, args.stitched_contigs, stitcher_plot_path=args.plot)
     args.contigs.close()
     args.stitched_contigs.close()

micall/core/denovo.py

@@ -19,7 +19,7 @@
 from Bio.SeqRecord import SeqRecord
 
 from micall.core.project_config import ProjectConfig
-from micall.core.contig_stitcher import GenotypedContig, stitch_consensus, logger as stitcher_logger, with_fresh_context
+from micall.core.contig_stitcher import GenotypedContig, stitch_consensus, with_fresh_context
 from micall.core.plot_contigs import plot_stitcher_coverage
 from micall.utils.structured_logger import add_structured_handler
 
@@ -98,7 +98,7 @@ def run_stitcher(ctx):
                                  group_ref=contig.group_ref,
                                  contig=contig.seq))
 
-        if stitcher_logger.level <= logging.DEBUG and stitcher_plot_path is not None:
+        if stitcher_plot_path is not None:
             plot_stitcher_coverage(ctx.events, stitcher_plot_path)
 
         return len(contigs)