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@jermp
jermp committed Mar 21, 2024
1 parent 8d234bf commit c919802
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Showing 2 changed files with 47 additions and 25 deletions.
54 changes: 35 additions & 19 deletions include/dictionary.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,42 +106,57 @@ 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, 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, 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, bool check_reverse_complement) const {
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,
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,
bool check_reverse_complement) const {
kmer_t uint_kmer = util::string_to_uint_kmer(string_kmer, m_k);
return kmer_forward_neighbours(uint_kmer, check_reverse_complement);
}
neighbourhood dictionary::kmer_forward_neighbours(kmer_t uint_kmer, bool check_reverse_complement) 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, check_reverse_complement);
return res;
}

neighbourhood dictionary::kmer_backward_neighbours(char const* string_kmer, bool check_reverse_complement) 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, check_reverse_complement);
}
neighbourhood dictionary::kmer_backward_neighbours(kmer_t uint_kmer, bool check_reverse_complement) 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, check_reverse_complement);
return res;
}

neighbourhood dictionary::kmer_neighbours(char const* string_kmer, bool check_reverse_complement) 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, check_reverse_complement);
}
Expand All @@ -154,7 +169,8 @@ neighbourhood dictionary::kmer_neighbours(kmer_t uint_kmer, bool check_reverse_c
return res;
}

neighbourhood dictionary::contig_neighbours(uint64_t contig_id, bool check_reverse_complement) 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);
Expand Down
18 changes: 12 additions & 6 deletions include/dictionary.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,13 +40,18 @@ struct dictionary {
uint64_t contig_size(uint64_t contig_id) const;

/* Navigational queries. */
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;
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, bool check_reverse_complement = true) 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;

Expand Down Expand Up @@ -119,7 +124,8 @@ 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, bool check_reverse_complement) const;
void backward_neighbours(kmer_t prefix, 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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