whoops, fix dropping on ref instead of alt... also handle ref more el…

…egantly

msyd/pyxfiles/coords.pyx

@@ -322,10 +322,15 @@ class Pansyn:
         Returns a new `Pansyn` object with `start`/`end` positions from the start/end of this pansyntenic region removed counting on `org`, respecting cigar alignments if not `None`.
         If this `Pansyn` has no cigar object, it will be identical to a drop on the reference (as the genomes are assumed to align perfectly).
         """
+        # in case its called with the ref org already, directly drop
+        # this fn shouldn't usually be called like this, but handle anyway
+        if org == self.ref.org:
+            return self.drop(start, end)
+
         assert(org in self.ranges_dict)
         # get no of bases corresponding to this drop on the reference
         if self.cigars_dict:
-            start, end = self.cigars_dict[org].trim(start, end, only_pos=True)
+            start, end = self.cigars_dict[org].trim(start, end, only_pos=True, ref=False)
 
         return self.drop(start, end)