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Linting nanopore.cpp #333

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Merged
andrewdavidsmith merged 1 commit into from
Jan 1, 2026
Merged

Linting nanopore.cpp #333

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15 changes: 11 additions & 4 deletions src/analysis/nanopore.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@
#include <utility>
#include <vector>

// NOLINTBEGIN(*-narrowing-conversions,*-pointer-arithmetic)
// NOLINTBEGIN(*-narrowing-conversions)

// clang-format off
static constexpr std::array<std::uint8_t, 256> encoding = {
Expand Down Expand Up @@ -315,6 +315,7 @@ struct mod_prob_buffer {

int n_types{};
const auto types = bam_mods_recorded(m.get(), &n_types);
// NOLINTNEXTLINE(*-pointer-arithmetic)
if (n_types < 2 || (types[h_idx] != 'h' && types[m_idx] != 'm'))
return false;

Expand All @@ -337,7 +338,8 @@ count_states_fwd(const bamxx::bam_rec &aln, std::vector<CountSet> &counts,
/* Move through cigar, reference and read positions without
inflating cigar or read sequence */
const auto beg_cig = bam_get_cigar(aln);
const auto end_cig = beg_cig + get_n_cigar(aln);
const auto end_cig =
beg_cig + get_n_cigar(aln); // NOLINT(*-pointer-arithmetic)

auto rpos = get_pos(aln);
auto ref_itr = std::cbegin(chrom) + rpos;
Expand Down Expand Up @@ -386,7 +388,8 @@ count_states_rev(const bamxx::bam_rec &aln, std::vector<CountSet> &counts,
/* Move through cigar, reference and (*backward*) through read
positions without inflating cigar or read sequence */
const auto beg_cig = bam_get_cigar(aln);
const auto end_cig = beg_cig + get_n_cigar(aln);
const auto end_cig =
beg_cig + get_n_cigar(aln); // NOLINT(*-pointer-arithmetic)

auto rpos = get_pos(aln);
auto ref_itr = std::cbegin(chrom) + rpos;
Expand Down Expand Up @@ -440,6 +443,7 @@ get_tid_to_idx(
for (std::int32_t i = 0; i < get_n_targets(hdr); ++i) {
// "curr_name" gives a "tid_to_name" mapping allowing to jump
// through "name_to_idx" and get "tid_to_idx"
// NOLINTNEXTLINE(*-pointer-arithmetic)
const std::string curr_name(hdr.h->target_name[i]);
const auto name_itr(name_to_idx.find(curr_name));
if (name_itr == std::cend(name_to_idx))
Expand Down Expand Up @@ -521,6 +525,7 @@ struct mod_prob_stats {

int n_types{};
const auto types = bam_mods_recorded(m.get(), &n_types);
// NOLINTNEXTLINE(*-pointer-arithmetic)
if (n_types < 2 || (types[h_idx] != 'h' && types[m_idx] != 'm'))
return;

Expand Down Expand Up @@ -943,6 +948,7 @@ valid_modification_types(const std::string &infile,
int n_types{};
const auto types = bam_mods_recorded(m.get(), &n_types);
// clang-format off
// NOLINTBEGIN(*-pointer-arithmetic)
valid_types = ((n_types == 0) ||
(n_types == 1 && types[0] == 'C') ||
(n_types >= 2 && types[0] == 'h' && types[1] == 'm'));
Expand All @@ -953,6 +959,7 @@ valid_modification_types(const std::string &infile,
message += "type[" + std::to_string(i) +
"]=" + std::to_string(static_cast<char>(types[i])) + "\n";
}
// NOLINTEND(*-pointer-arithmetic)
}
return std::make_pair(valid_types, message);
}
Expand Down Expand Up @@ -1111,6 +1118,6 @@ main_nanocount(int argc, char *argv[]) { // NOLINT(*-avoid-c-arrays)
return EXIT_SUCCESS;
}

// NOLINTEND(*-narrowing-conversions,*-pointer-arithmetic)
// NOLINTEND(*-narrowing-conversions)

#endif