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Merge pull request #43 from hmusta/hmusta/traversal_fix
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Allow for ignoring reverse complements when checking neighbours
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@jermp
jermp authored Feb 19, 2024
2 parents fd771a0 + 49966c8 commit 5a13d6a
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Showing 2 changed files with 35 additions and 35 deletions.
52 changes: 26 additions & 26 deletions include/dictionary.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -106,61 +106,61 @@ uint64_t dictionary::contig_size(uint64_t contig_id) const {
return contig_length - m_k + 1;
}

void dictionary::forward_neighbours(kmer_t suffix, neighbourhood& res) const {
res.forward_A = lookup_advanced_uint(suffix + (util::char_to_uint('A') << (2 * (m_k - 1))));
res.forward_C = lookup_advanced_uint(suffix + (util::char_to_uint('C') << (2 * (m_k - 1))));
res.forward_G = lookup_advanced_uint(suffix + (util::char_to_uint('G') << (2 * (m_k - 1))));
res.forward_T = lookup_advanced_uint(suffix + (util::char_to_uint('T') << (2 * (m_k - 1))));
void dictionary::forward_neighbours(kmer_t suffix, neighbourhood& res, bool check_reverse_complement) const {
res.forward_A = lookup_advanced_uint(suffix + (util::char_to_uint('A') << (2 * (m_k - 1))), check_reverse_complement);
res.forward_C = lookup_advanced_uint(suffix + (util::char_to_uint('C') << (2 * (m_k - 1))), check_reverse_complement);
res.forward_G = lookup_advanced_uint(suffix + (util::char_to_uint('G') << (2 * (m_k - 1))), check_reverse_complement);
res.forward_T = lookup_advanced_uint(suffix + (util::char_to_uint('T') << (2 * (m_k - 1))), check_reverse_complement);
}
void dictionary::backward_neighbours(kmer_t prefix, neighbourhood& res) const {
res.backward_A = lookup_advanced_uint(prefix + util::char_to_uint('A'));
res.backward_C = lookup_advanced_uint(prefix + util::char_to_uint('C'));
res.backward_G = lookup_advanced_uint(prefix + util::char_to_uint('G'));
res.backward_T = lookup_advanced_uint(prefix + util::char_to_uint('T'));
void dictionary::backward_neighbours(kmer_t prefix, neighbourhood& res, bool check_reverse_complement) const {
res.backward_A = lookup_advanced_uint(prefix + util::char_to_uint('A'), check_reverse_complement);
res.backward_C = lookup_advanced_uint(prefix + util::char_to_uint('C'), check_reverse_complement);
res.backward_G = lookup_advanced_uint(prefix + util::char_to_uint('G'), check_reverse_complement);
res.backward_T = lookup_advanced_uint(prefix + util::char_to_uint('T'), check_reverse_complement);
}

neighbourhood dictionary::kmer_forward_neighbours(char const* string_kmer) const {
neighbourhood dictionary::kmer_forward_neighbours(char const* string_kmer, bool check_reverse_complement) const {
kmer_t uint_kmer = util::string_to_uint_kmer(string_kmer, m_k);
return kmer_forward_neighbours(uint_kmer);
return kmer_forward_neighbours(uint_kmer, check_reverse_complement);
}
neighbourhood dictionary::kmer_forward_neighbours(kmer_t uint_kmer) const {
neighbourhood dictionary::kmer_forward_neighbours(kmer_t uint_kmer, bool check_reverse_complement) const {
neighbourhood res;
kmer_t suffix = uint_kmer >> 2;
forward_neighbours(suffix, res);
forward_neighbours(suffix, res, check_reverse_complement);
return res;
}

neighbourhood dictionary::kmer_backward_neighbours(char const* string_kmer) const {
neighbourhood dictionary::kmer_backward_neighbours(char const* string_kmer, bool check_reverse_complement) const {
kmer_t uint_kmer = util::string_to_uint_kmer(string_kmer, m_k);
return kmer_backward_neighbours(uint_kmer);
return kmer_backward_neighbours(uint_kmer, check_reverse_complement);
}
neighbourhood dictionary::kmer_backward_neighbours(kmer_t uint_kmer) const {
neighbourhood dictionary::kmer_backward_neighbours(kmer_t uint_kmer, bool check_reverse_complement) const {
neighbourhood res;
kmer_t prefix = (uint_kmer << 2) & ((kmer_t(1) << (2 * m_k)) - 1);
backward_neighbours(prefix, res);
backward_neighbours(prefix, res, check_reverse_complement);
return res;
}

neighbourhood dictionary::kmer_neighbours(char const* string_kmer) const {
neighbourhood dictionary::kmer_neighbours(char const* string_kmer, bool check_reverse_complement) const {
kmer_t uint_kmer = util::string_to_uint_kmer(string_kmer, m_k);
return kmer_neighbours(uint_kmer);
return kmer_neighbours(uint_kmer, check_reverse_complement);
}
neighbourhood dictionary::kmer_neighbours(kmer_t uint_kmer) const {
neighbourhood dictionary::kmer_neighbours(kmer_t uint_kmer, bool check_reverse_complement) const {
neighbourhood res;
kmer_t suffix = uint_kmer >> 2;
forward_neighbours(suffix, res);
forward_neighbours(suffix, res, check_reverse_complement);
kmer_t prefix = (uint_kmer << 2) & ((kmer_t(1) << (2 * m_k)) - 1);
backward_neighbours(prefix, res);
backward_neighbours(prefix, res, check_reverse_complement);
return res;
}

neighbourhood dictionary::contig_neighbours(uint64_t contig_id) const {
neighbourhood dictionary::contig_neighbours(uint64_t contig_id, bool check_reverse_complement) const {
assert(contig_id < num_contigs());
neighbourhood res;
kmer_t suffix = m_buckets.contig_suffix(contig_id, m_k);
forward_neighbours(suffix, res);
forward_neighbours(suffix, res, check_reverse_complement);
kmer_t prefix = m_buckets.contig_prefix(contig_id, m_k) << 2;
backward_neighbours(prefix, res);
backward_neighbours(prefix, res, check_reverse_complement);
return res;
}

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18 changes: 9 additions & 9 deletions include/dictionary.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -40,15 +40,15 @@ struct dictionary {
uint64_t contig_size(uint64_t contig_id) const;

/* Navigational queries. */
neighbourhood kmer_forward_neighbours(char const* string_kmer) const;
neighbourhood kmer_forward_neighbours(kmer_t uint_kmer) const;
neighbourhood kmer_backward_neighbours(char const* string_kmer) const;
neighbourhood kmer_backward_neighbours(kmer_t uint_kmer) const;
neighbourhood kmer_forward_neighbours(char const* string_kmer, bool check_reverse_complement = true) const;
neighbourhood kmer_forward_neighbours(kmer_t uint_kmer, bool check_reverse_complement = true) const;
neighbourhood kmer_backward_neighbours(char const* string_kmer, bool check_reverse_complement = true) const;
neighbourhood kmer_backward_neighbours(kmer_t uint_kmer, bool check_reverse_complement = true) const;

/* forward and backward */
neighbourhood kmer_neighbours(char const* string_kmer) const;
neighbourhood kmer_neighbours(kmer_t uint_kmer) const;
neighbourhood contig_neighbours(uint64_t contig_id) const;
neighbourhood kmer_neighbours(char const* string_kmer, bool check_reverse_complement = true) const;
neighbourhood kmer_neighbours(kmer_t uint_kmer, bool check_reverse_complement = true) const;
neighbourhood contig_neighbours(uint64_t contig_id, bool check_reverse_complement = true) const;

/* Return the weight of the kmer given its id. */
uint64_t weight(uint64_t kmer_id) const;
Expand Down Expand Up @@ -118,8 +118,8 @@ struct dictionary {

lookup_result lookup_uint_regular_parsing(kmer_t uint_kmer) const;
lookup_result lookup_uint_canonical_parsing(kmer_t uint_kmer) const;
void forward_neighbours(kmer_t suffix, neighbourhood& res) const;
void backward_neighbours(kmer_t prefix, neighbourhood& res) const;
void forward_neighbours(kmer_t suffix, neighbourhood& res, bool check_reverse_complement) const;
void backward_neighbours(kmer_t prefix, neighbourhood& res, bool check_reverse_complement) const;
};

} // namespace sshash

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