Improve support for eland searching a single fasta containing multiple records.

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder_ipar100.py

diff --git a/htsworkflow/pipelines/test/test_runfolder_ipar100.py b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
index 4f07effdae3bce929935ddfa53daa484ca1d7c72..bf1b520124ab11c01c0ce2a39f39a8d9e83e8cd4 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_ipar100.py
+++ b/htsworkflow/pipelines/test/test_runfolder_ipar100.py
@@ -220,12 +220,14 @@ class RunfolderTests(unittest.TestCase):
 
         for i in range(1,9):
             lane = eland.results[0][i]
-            self.failUnlessEqual(lane.reads, 4)
+            self.failUnlessEqual(lane.reads, 6)
             self.failUnlessEqual(lane.sample_name, "s")
             self.failUnlessEqual(lane.lane_id, i)
-            self.failUnlessEqual(len(lane.mapped_reads), 15)
+            self.failUnlessEqual(len(lane.mapped_reads), 17)
             self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
-            self.failUnlessEqual(lane.match_codes['U0'], 1)
+            self.failUnlessEqual(lane.mapped_reads['spike.fa/sample1'], 1)
+            self.failUnlessEqual(lane.mapped_reads['spike.fa/sample2'], 1)
+            self.failUnlessEqual(lane.match_codes['U0'], 3)
             self.failUnlessEqual(lane.match_codes['R0'], 2)
             self.failUnlessEqual(lane.match_codes['U1'], 1)
             self.failUnlessEqual(lane.match_codes['R1'], 9)
@@ -246,7 +248,7 @@ class RunfolderTests(unittest.TestCase):
             self.failUnlessEqual(l1.sample_name, l2.sample_name)
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
-            self.failUnlessEqual(len(l1.mapped_reads), 15)
+            self.failUnlessEqual(len(l1.mapped_reads), 17)
             for k in l1.mapped_reads.keys():
                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])