rename option + man

README.md

@@ -421,6 +421,9 @@ We recommend to not modify these options unless you are clearly aware of their e
 `--no_secondary`
     Ignore secondary alignments.
 
+`--report_unstranded`
+    Report transcripts for which the strand cannot be detected using canonical splice sites.
+
 `--aligner`
     Force to use this alignment method, can be `starlong` or `minimap2`; `minimap2` is currently used as default. Make sure the specified aligner is in the `$PATH` variable.
 

isoquant.py

@@ -140,7 +140,7 @@ def add_hidden_option(*args, **kwargs):  # show command only with --full-help
 
     parser.add_argument('--check_canonical', action='store_true', default=False,
                         help="report whether splice junctions are canonical")
-    add_additional_option("--keep_noncanonical", help="report transcripts for which the strand cannot be detected "
+    add_additional_option("--report_unstranded", help="report transcripts for which the strand cannot be detected "
                                                       "using canonical splice sites",
                           action='store_true', default=False)
     parser.add_argument("--sqanti_output", help="produce SQANTI-like TSV output",

src/graph_based_model_construction.py

@@ -379,7 +379,7 @@ def construct_fl_isoforms(self):
                 elif len(novel_exons) == 2 and (not polya_site or transcript_ss_strand == '.'):
                     # logger.debug("uuu Avoiding single intron %s isoform: %d\t%s" % (new_transcript_id, count, str(path)))
                     pass
-                elif transcript_strand == '.' and not self.params.keep_noncanonical:
+                elif transcript_strand == '.' and not self.params.report_unstranded:
                     logger.info("Avoiding unreliable transcript with %d exons" % len(novel_exons))
                     pass
                 else: