fix temporary assert

src/graph_based_model_construction.py

@@ -132,9 +132,10 @@ def process(self, read_assignment_storage):
         self.assign_reads_to_models(read_assignment_storage)
         self.forward_counts()
 
-        if len(set([x.read_id for x in read_assignment_storage])) != len(self.read_assignment_counts):
+        # FIXME: remove asserts below
+        if self.transcript_model_storage and len(set([x.read_id for x in read_assignment_storage])) != len(self.read_assignment_counts):
             logger.warning("Some reads were not assigned %d %d" % (len(set([x.read_id for x in read_assignment_storage])), len(self.read_assignment_counts)))
-
+        # FIXME: remove asserts below
         if any(value < 0 for value in self.read_assignment_counts.values()):
             logger.warning("Negative values in read assignment counts")
 
@@ -396,7 +397,7 @@ def construct_fl_isoforms(self):
                     # 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.report_unstranded:
-                    logger.info("Avoiding unreliable transcript with %d exons (strand cannot be detected)" % len(novel_exons))
+                    logger.debug("Avoiding unreliable transcript with %d exons (strand cannot be detected)" % len(novel_exons))
                     pass
                 else:
                     if self.params.use_technical_replicas and \