Fix bug with noduplicateseqs method not updating sequence number

althonos · May 13, 2024 · 45bbb67 · 45bbb67
1 parent 556fbbf
commit 45bbb67
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Showing 2 changed files with 14 additions and 1 deletion.
diff --git a/patches/Cleaner.cpp.patch b/patches/Cleaner.cpp.patch
@@ -0,0 +1,14 @@
+--- a/source/Cleaner.cpp
++++ b/source/Cleaner.cpp
+@@ -1466,7 +1466,10 @@
+         {
+             if (alig->sequences[i] == alig->sequences[x])
+             {
+-                alig->saveSequences[i] = -1;
++                if (alig->saveSequences[i] != -1) {
++                    alig->saveSequences[i] = -1;
++                    alig->numberOfSequences--;
++                }
+                 debug.report(InfoCode::RemovingDuplicateSequences,
+                         new std::string[2] {
+                     alig->seqsName[i],
diff --git a/pytrimal/tests/test_automatic_trimmer.py b/pytrimal/tests/test_automatic_trimmer.py
@@ -59,7 +59,6 @@ def test_gappyout_method(self):
 
     @unittest.skipIf(sys.version_info < (3, 6), "No pathlib support in Python 3.5")
     @unittest.skipUnless(files, "importlib.resources.files not available")
-    @unittest.expectedFailure
     def test_noduplicateseqs_method(self):
         self._test_method("noduplicateseqs")