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surject: realign anchors containing substitutions #5010

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surject: realign anchors containing substitutions #5010

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13 changes: 13 additions & 0 deletions src/surjector.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3403,13 +3403,26 @@ using namespace std;
}
#endif
auto normal_aligner = get_aligner(!source.quality().empty());
bool chunk_has_substitution = false;
if (mp_aln_path_chunks->size() == 1) {
const auto& chunk_path = mp_aln_path_chunks->front().second;
for (size_t i = 0; i < chunk_path.mapping_size() && !chunk_has_substitution; ++i) {
for (const auto& edit : chunk_path.mapping(i).edit()) {
chunk_has_substitution = chunk_has_substitution ||
(edit.from_length() != 0 && edit.to_length() != 0 && !edit.sequence().empty());
}
}
}
// check whether it's necessary to do any alignment in this interval
if (mp_aln_path_chunks->size() == 1 &&
!chunk_has_substitution &&
mp_aln_path_chunks->front().first.first == mp_aln_source->sequence().begin() &&
mp_aln_path_chunks->front().first.second == mp_aln_source->sequence().end()) {
#ifdef debug_anchored_surject
cerr << "chunk constitutes full alignment of this interval, no need for multipath alignment" << endl;
#endif
surjected_aln.set_sequence(mp_aln_source->sequence());
surjected_aln.set_quality(mp_aln_source->quality());
to_proto_path(mp_aln_path_chunks->front().second, *surjected_aln.mutable_path());
surjected_aln.set_score(normal_aligner->scorer->score_contiguous_alignment(surjected_aln));
// TODO: it should be possible to rely on the ref chunks here rather than using the path scan later
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