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Only keeping strobemer matches with minimum strobes distance difference #517

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Only keeping strobemer matches with minimum strobes distance difference #517

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21 changes: 17 additions & 4 deletions src/chain.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -17,17 +17,30 @@ void add_to_anchors_full(
size_t position
) {
int min_diff = std::numeric_limits<int>::max();
std::vector<size_t> best_positions;

for (const auto hash = index.get_hash(position); index.get_hash(position) == hash; ++position) {
int ref_start = index.get_strobe1_position(position);
int ref_end = ref_start + index.strobe2_offset(position) + index.k();
int diff = std::abs((query_end - query_start) - (ref_end - ref_start));
if (diff <= min_diff) {
int ref_idx = index.reference_index(position);
anchors.push_back({uint(query_start), uint(ref_start), uint(ref_idx)});
anchors.push_back({uint(query_end - index.k()), uint(ref_end - index.k()), uint(ref_idx)});

if (diff < min_diff) {
min_diff = diff;
best_positions.clear();
best_positions.push_back(position);
} else if (diff == min_diff) {
best_positions.push_back(position);
}
}

for (size_t pos : best_positions) {
int ref_start = index.get_strobe1_position(pos);
int ref_end = ref_start + index.strobe2_offset(pos) + index.k();
int ref_idx = index.reference_index(pos);

anchors.push_back({uint(query_start), uint(ref_start), uint(ref_idx)});
anchors.push_back({uint(query_end - index.k()), uint(ref_end - index.k()), uint(ref_idx)});
}
}

void add_to_anchors_partial(
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