diff jbrowse2.py @ 27:4ff1ed2065cc draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty

--- a/jbrowse2.py	Sat Feb 03 22:22:07 2024 +0000
+++ b/jbrowse2.py	Wed Feb 07 22:37:10 2024 +0000
@@ -1224,7 +1224,7 @@
                 self.add_paf(
                     dataset_path,
                     outputTrackConfig,
-                    track["conf"]["options"]["synteny"],
+                    track["conf"]["options"]["paf"],
                 )
             else:
                 log.warn("Do not know how to handle %s", dataset_ext)
@@ -1279,6 +1279,7 @@
         if data.get("defaultLocation", ""):
             ddl = data["defaultLocation"]
             loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
+            # allow commas like 100,000 but ignore as integer
             if loc_match:
                 refName = loc_match.group(1)
                 drdict["refName"] = refName
@@ -1291,12 +1292,6 @@
                     "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                     % ddl
                 )
-        elif self.genome_firstcontig is not None:
-            drdict["refName"] = self.genome_firstcontig
-            logging.info(
-                "@@@ no defaultlocation found for default session - using %s as first contig found"
-                % self.genome_firstcontig
-            )
 
         if drdict.get("refName", None):
             # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome