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swap locate query with string checking in lookup #85

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Merged
jermp merged 1 commit into from
Jan 21, 2026
Merged

swap locate query with string checking in lookup #85

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34 changes: 15 additions & 19 deletions include/spectrum_preserving_string_set.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -219,19 +219,18 @@ struct spectrum_preserving_string_set //

res.kmer_offset = p.absolute_offset - mini_info.pos_in_kmer;

if (res.kmer_offset >= res.string_begin and res.kmer_offset < res.string_end) {
if (kmer != util::read_kmer_at<Kmer>(strings, k, Kmer::bits_per_char * res.kmer_offset)) {
return false;
}

if (res.kmer_offset >= res.string_begin and res.kmer_offset < res.string_end - k + 1) {
res.kmer_id = res.kmer_offset - res.string_id * (k - 1); // absolute kmer id
res.kmer_id_in_string = res.kmer_offset - res.string_begin; // relative kmer id
} else {
strings_offsets.offset_to_id(res, p, k);
}

if (res.kmer_offset >= res.string_begin and res.kmer_offset < res.string_end - k + 1 and //
kmer == util::read_kmer_at<Kmer>(strings, k, Kmer::bits_per_char * res.kmer_offset)) //
{
return true;
}

if (res.kmer_offset < res.string_end - k + 1) return true;
return false;
}

Expand All @@ -257,24 +256,21 @@ struct spectrum_preserving_string_set //

res.kmer_offset = p.absolute_offset - pos_in_kmer;

if (res.kmer_offset >= res.string_begin and res.kmer_offset < res.string_end) {
auto read_kmer =
util::read_kmer_at<Kmer>(strings, k, Kmer::bits_per_char * res.kmer_offset);
if (read_kmer != kmer and read_kmer != kmer_rc) return false;

res.kmer_orientation =
read_kmer == kmer_rc ? constants::backward_orientation : constants::forward_orientation;

if (res.kmer_offset >= res.string_begin and res.kmer_offset < res.string_end - k + 1) {
res.kmer_id = res.kmer_offset - res.string_id * (k - 1); // absolute kmer id
res.kmer_id_in_string = res.kmer_offset - res.string_begin; // relative kmer id
} else {
strings_offsets.offset_to_id(res, p, k);
}

if (res.kmer_offset >= res.string_begin and res.kmer_offset < res.string_end - k + 1) //
{
auto read_kmer =
util::read_kmer_at<Kmer>(strings, k, Kmer::bits_per_char * res.kmer_offset);
if (read_kmer == kmer) return true;
if (read_kmer == kmer_rc) {
res.kmer_orientation = constants::backward_orientation;
return true;
}
}

if (res.kmer_offset < res.string_end - k + 1) return true;
return false;
}
};
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