From 0a232822922a006fd97ee9d6e94d44db733eca5d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Juri=C4=8D?= <499542@mail.muni.cz>
Date: Fri, 8 Sep 2023 12:34:49 +0200
Subject: [PATCH] Fixed minor issues and tests

---
 htsinfer/cli.py                  |  4 ++--
 htsinfer/get_library_type.py     |  5 +++--
 htsinfer/get_read_orientation.py |  1 -
 tests/test_get_library_type.py   | 15 +--------------
 4 files changed, 6 insertions(+), 19 deletions(-)

diff --git a/htsinfer/cli.py b/htsinfer/cli.py
index 99cb9ad6..e0735ce3 100644
--- a/htsinfer/cli.py
+++ b/htsinfer/cli.py
@@ -222,7 +222,7 @@ def __call__(
             "upper limit on the difference in the reference "
             "sequence coordinates between the two mates to be "
             "considered as coming from a single fragment "
-            "(Used only when sequence identifiers do not match) "
+            "(used only when sequence identifiers do not match) "
         )
     )
     parser.add_argument(
@@ -234,7 +234,7 @@ def __call__(
         help=(
             "minimum fraction of mates that can be mapped to compatible loci "
             "and are considered concordant pairs / all mates"
-            "(Used only when sequence identifiers do not match)"
+            "(used only when sequence identifiers do not match)"
         )
     )
     parser.add_argument(
diff --git a/htsinfer/get_library_type.py b/htsinfer/get_library_type.py
index c341d4f8..ba8d64da 100644
--- a/htsinfer/get_library_type.py
+++ b/htsinfer/get_library_type.py
@@ -124,8 +124,9 @@ def _evaluate_mate_relationship(
                 self.results.relationship = (
                     StatesTypeRelationship.split_mates
                 )
-                self.mapping.library_type.relationship \
-                    = StatesTypeRelationship.split_mates
+                self.mapping.library_type.relationship = (
+                    StatesTypeRelationship.split_mates
+                )
         else:
             self.mapping.library_type.relationship \
                 = StatesTypeRelationship.not_available
diff --git a/htsinfer/get_read_orientation.py b/htsinfer/get_read_orientation.py
index cacd141f..d76b0922 100644
--- a/htsinfer/get_read_orientation.py
+++ b/htsinfer/get_read_orientation.py
@@ -101,7 +101,6 @@ def process_alignments(
             if star_dirs[0].name == "file_1":
                 results.file_1 = self.process_single(sam=paths[0])
         elif len(star_dirs) == 2:
-            print("Getting there")
             results.file_1 = self.process_single(sam=paths[0])
             results.file_2 = self.process_single(sam=paths[1])
         return results
diff --git a/tests/test_get_library_type.py b/tests/test_get_library_type.py
index 7651d165..65fd76eb 100644
--- a/tests/test_get_library_type.py
+++ b/tests/test_get_library_type.py
@@ -124,20 +124,7 @@ def test_evaluate_mate_relationship_not_mates(self):
                                    mapping=MAPPING)
         test_instance.results.file_1 = StatesType.first_mate
         test_instance.results.file_2 = StatesType.second_mate
-        test_instance._evaluate_mate_relationship(
-            ids_1=["A", "B", "C"],
-            ids_2=["C", "B", "A"],
-        )
-        assert (
-            test_instance.results.relationship ==
-            StatesTypeRelationship.not_mates
-        )
-        test_instance.results.file_1 = StatesType.single
-        test_instance.results.file_2 = StatesType.first_mate
-        test_instance._evaluate_mate_relationship(
-            ids_1=["A", "B", "C"],
-            ids_2=["A", "B", "C"],
-        )
+        test_instance.evaluate()
         assert (
             test_instance.results.relationship ==
             StatesTypeRelationship.not_mates