Contig stitcher: simplify the munge operation

Use strip_query operations to avoid coordinate arithmetic.
cfe-lab · Nov 15, 2023 · 4d61b41 · 4d61b41
1 parent ea58060
commit 4d61b41
Showing 1 changed file with 7 additions and 9 deletions.
diff --git a/micall/core/contig_stitcher.py b/micall/core/contig_stitcher.py
@@ -167,22 +167,20 @@ def cut_reference(self, cut_point: float) -> 'FrankensteinContig':
 
     @staticmethod
     def munge(left: AlignedContig, right: AlignedContig) -> AlignedContig:
-        left_query_seq = left.seq[0:left.alignment.q_ei + 1]
-        right_query_seq = right.seq[right.alignment.q_st:]
-        query_seq = left_query_seq + right_query_seq
+        query_seq = left.rstrip_query().seq + right.lstrip_query().seq
+        query = GenotypedContig(seq=query_seq,
+                                name=f'{left.name}+{right.name}',
+                                ref_name=left.ref_name,
+                                ref_seq=left.ref_seq,
+                                matched_fraction=None)
 
         left_alignment = left.alignment
         right_alignment = \
             right.alignment.translate(
-                query_delta=(-1 * right.alignment.q_st + len(left_query_seq)),
+                query_delta=(-1 * right.alignment.q_st + left.alignment.q_ei + 1),
                 reference_delta=0)
         alignment = left_alignment.connect(right_alignment)
 
-        query = GenotypedContig(seq=query_seq,
-                                name=f'{left.name}+{right.name}',
-                                ref_name=left.ref_name,
-                                ref_seq=left.ref_seq,
-                                matched_fraction=None)
         return AlignedContig(query, alignment)