Contig stitcher: improve alignment visualisation

Make sure that alignment does not go outside the range of the reference sequence.
cfe-lab · Jan 22, 2024 · 6f94af8 · 6f94af8
1 parent 135ef59
commit 6f94af8
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Showing 2 changed files with 20 additions and 18 deletions.
diff --git a/micall/core/plot_contigs.py b/micall/core/plot_contigs.py
@@ -787,6 +787,7 @@ def get_neighbour(part, lookup):
                 else:
                     start_delta = -1 * part.alignment.q_st
                 r_st = part.alignment.r_st + start_delta + position_offset
+                r_st = max(r_st, 0)
 
             if next_part is not None:
                 r_ei = next_part.alignment.r_ei + position_offset
@@ -796,6 +797,7 @@ def get_neighbour(part, lookup):
                 else:
                     end_delta = len(part.seq) - 1 - part.alignment.q_ei
                 r_ei = part.alignment.r_ei + end_delta + position_offset
+                r_ei = min(r_ei, len(part.ref_seq) + position_offset)
 
             aligned_size_map[part.name] = (r_st, r_ei)
 

diff --git a/...a/stitcher_plots/test_partial_align_consensus_multiple_overlaping_sequences.svg b/...a/stitcher_plots/test_partial_align_consensus_multiple_overlaping_sequences.svg