Contig stitcher: simplify overlap seq calculation

cfe-lab · Nov 15, 2023 · 713df5d · 713df5d
1 parent 6d44808
commit 713df5d
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/micall/core/contig_stitcher.py b/micall/core/contig_stitcher.py
@@ -248,9 +248,11 @@ def stitch_2_contigs(left, right):
     # Cut in 4 parts.
     left_remainder, left_overlap = left.cut_reference(right.alignment.r_st - 0.5)
     right_overlap, right_remainder = right.cut_reference(left.alignment.r_ei + 0.5)
+    left_overlap = left_overlap.rstrip_query()
+    right_overlap = right_overlap.lstrip_query()
 
     # Align overlapping parts, then recombine based on concordance.
-    aligned_left, aligned_right = align_queries(left_overlap.aligned_seq, right_overlap.aligned_seq)
+    aligned_left, aligned_right = align_queries(left_overlap.seq, right_overlap.seq)
     concordance = calculate_concordance(aligned_left, aligned_right)
     max_concordance_index = max(range(len(concordance)),
                                 key=lambda i: concordance[i])