The summary parsing code now seems to handle paired end runs

[htsworkflow.git] / htsworkflow / pipelines / gerald.py

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index 7e2328ad3b7613f1886accef135e0698082f12ba..a5dd323861beb46549fc3b98be0f6af77eec6e84 100644 (file)
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -88,7 +88,8 @@ class Gerald(object):
             # those consistently.
             for element in analysis:
                 sample, lane_id = element.tag.split('_')
-                self._lanes[lane_id] = Gerald.LaneParameters(self._gerald, lane_id)
+                self._lanes[int(lane_id)] = Gerald.LaneParameters(
+                                              self._gerald, lane_id)
 
         def __getitem__(self, key):
             if self._lane is None:
@@ -201,4 +202,4 @@ if __name__ == "__main__":
   # quick test code
   import sys
   g = gerald(sys.argv[1])
-  #ElementTree.dump(g.get_elements())
\ No newline at end of file
+  #ElementTree.dump(g.get_elements())