return to before, make ref2binary okay for Ns

cbg-ethz · Apr 26, 2024 · 1def5e8 · 1def5e8
1 parent e429bd0
commit 1def5e8
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Showing 4 changed files with 7 additions and 6 deletions.
diff --git a/tests/test_tiling.py b/tests/test_tiling.py
@@ -26,7 +26,7 @@ def test_equispaced_use_full_reference_as_region():
 
     assert actual[0][0] == 1
     assert actual[0][1] == 201
-    assert actual[-1][0] == 2748 #2949 #2748 (old number where last windows where excluded)
+    assert actual[-1][0] == 2949 #2748 (old number where last windows where excluded)
     #assert actual[-1][0] + 201 < 3000
 
 

diff --git a/viloca/local_haplotype_inference/learn_error_params/preparation.py b/viloca/local_haplotype_inference/learn_error_params/preparation.py
@@ -103,5 +103,6 @@ def reference2binary(reference_seq, alphabet):
     length_seq = len(reference_seq)
     reference_table = np.zeros((length_seq, len(alphabet)))
     for base_position, base in enumerate(str(reference_seq)):
-        reference_table[base_position][alphabet.index(base.upper())] = 1
+        if alphabet.find(base) >= 0:
+            reference_table[base_position][alphabet.index(base.upper())] = 1
     return reference_table
diff --git a/viloca/local_haplotype_inference/use_quality_scores/preparation.py b/viloca/local_haplotype_inference/use_quality_scores/preparation.py
@@ -158,5 +158,6 @@ def reference2binary(reference_seq, alphabet):
     length_seq = len(reference_seq)
     reference_table = np.zeros((length_seq, len(alphabet)))
     for base_position, base in enumerate(str(reference_seq)):
-        reference_table[base_position][alphabet.index(base.upper())] = 1
+        if alphabet.find(base) >= 0:
+            reference_table[base_position][alphabet.index(base.upper())] = 1
     return reference_table
diff --git a/viloca/tiling.py b/viloca/tiling.py
@@ -103,9 +103,8 @@ def get_window_tilings(self) -> List[Tuple[int, int]]:
                 self.end - 1,
                 self.incr
             ))
-            while window_positions[-1] + self.window_length >= self.end:
-                del window_positions[-1] # FIXME uncommented to create one single window
-                #window_positions.append(self.end - 1 - self.window_length)
+            #while window_positions[-1] + self.window_length >= self.end:
+            #    del window_positions[-1] # FIXME uncommented to create one single window
 
         else:
             window_positions = list(range(