Skip to content

Commit 992f2c3

Browse files
author
vlad0x00
committed
const and formatting
1 parent de9f1a2 commit 992f2c3

File tree

6 files changed

+47
-28
lines changed

6 files changed

+47
-28
lines changed

‎include/btllib/nthash.hpp‎

Lines changed: 32 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -675,10 +675,14 @@ BTLLIB_NTHASH_PEEK(
675675
peek(),
676676

677677
{
678-
const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(new uint64_t[blocks.size()]);
679-
const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(new uint64_t[blocks.size()]);
680-
const std::unique_ptr<uint64_t[]> forward_hash_tmp(new uint64_t[blocks.size()]);
681-
const std::unique_ptr<uint64_t[]> reverse_hash_tmp(new uint64_t[blocks.size()]);
678+
const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(
679+
new uint64_t[blocks.size()]);
680+
const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(
681+
new uint64_t[blocks.size()]);
682+
const std::unique_ptr<uint64_t[]> forward_hash_tmp(
683+
new uint64_t[blocks.size()]);
684+
const std::unique_ptr<uint64_t[]> reverse_hash_tmp(
685+
new uint64_t[blocks.size()]);
682686
std::memcpy(fh_no_monomers_tmp.get(),
683687
forward_hash.get(),
684688
blocks.size() * sizeof(uint64_t));
@@ -709,10 +713,14 @@ BTLLIB_NTHASH_PEEK(
709713
peek(char char_in),
710714

711715
{
712-
const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(new uint64_t[blocks.size()]);
713-
const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(new uint64_t[blocks.size()]);
714-
const std::unique_ptr<uint64_t[]> forward_hash_tmp(new uint64_t[blocks.size()]);
715-
const std::unique_ptr<uint64_t[]> reverse_hash_tmp(new uint64_t[blocks.size()]);
716+
const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(
717+
new uint64_t[blocks.size()]);
718+
const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(
719+
new uint64_t[blocks.size()]);
720+
const std::unique_ptr<uint64_t[]> forward_hash_tmp(
721+
new uint64_t[blocks.size()]);
722+
const std::unique_ptr<uint64_t[]> reverse_hash_tmp(
723+
new uint64_t[blocks.size()]);
716724
std::memcpy(fh_no_monomers_tmp.get(),
717725
forward_hash.get(),
718726
blocks.size() * sizeof(uint64_t));
@@ -744,10 +752,14 @@ BTLLIB_NTHASH_PEEK(
744752
peek_back(),
745753

746754
{
747-
const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(new uint64_t[blocks.size()]);
748-
const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(new uint64_t[blocks.size()]);
749-
const std::unique_ptr<uint64_t[]> forward_hash_tmp(new uint64_t[blocks.size()]);
750-
const std::unique_ptr<uint64_t[]> reverse_hash_tmp(new uint64_t[blocks.size()]);
755+
const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(
756+
new uint64_t[blocks.size()]);
757+
const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(
758+
new uint64_t[blocks.size()]);
759+
const std::unique_ptr<uint64_t[]> forward_hash_tmp(
760+
new uint64_t[blocks.size()]);
761+
const std::unique_ptr<uint64_t[]> reverse_hash_tmp(
762+
new uint64_t[blocks.size()]);
751763
std::memcpy(fh_no_monomers_tmp.get(),
752764
forward_hash.get(),
753765
blocks.size() * sizeof(uint64_t));
@@ -778,10 +790,14 @@ BTLLIB_NTHASH_PEEK(
778790
peek_back(char char_in),
779791

780792
{
781-
const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(new uint64_t[blocks.size()]);
782-
const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(new uint64_t[blocks.size()]);
783-
const std::unique_ptr<uint64_t[]> forward_hash_tmp(new uint64_t[blocks.size()]);
784-
const std::unique_ptr<uint64_t[]> reverse_hash_tmp(new uint64_t[blocks.size()]);
793+
const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(
794+
new uint64_t[blocks.size()]);
795+
const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(
796+
new uint64_t[blocks.size()]);
797+
const std::unique_ptr<uint64_t[]> forward_hash_tmp(
798+
new uint64_t[blocks.size()]);
799+
const std::unique_ptr<uint64_t[]> reverse_hash_tmp(
800+
new uint64_t[blocks.size()]);
785801
std::memcpy(fh_no_monomers_tmp.get(),
786802
forward_hash.get(),
787803
blocks.size() * sizeof(uint64_t));

‎include/btllib/nthash_lowlevel.hpp‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -123,7 +123,7 @@ ntf64(const char* kmer_seq, unsigned k)
123123
h_val ^= TRIMER_TAB[trimer_loc];
124124
} else if (remainder == 2) {
125125
const uint8_t dimer_loc = 4 * CONVERT_TAB[(unsigned char)kmer_seq[k - 2]] +
126-
CONVERT_TAB[(unsigned char)kmer_seq[k - 1]];
126+
CONVERT_TAB[(unsigned char)kmer_seq[k - 1]];
127127
h_val ^= DIMER_TAB[dimer_loc];
128128
} else if (remainder == 1) {
129129
h_val ^= SEED_TAB[(unsigned char)kmer_seq[k - 1]];
@@ -152,8 +152,9 @@ ntr64(const char* kmer_seq, unsigned k)
152152
RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 3]];
153153
h_val ^= TRIMER_TAB[trimer_loc];
154154
} else if (remainder == 2) {
155-
const uint8_t dimer_loc = 4 * RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 1]] +
156-
RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 2]];
155+
const uint8_t dimer_loc =
156+
4 * RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 1]] +
157+
RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 2]];
157158
h_val ^= DIMER_TAB[dimer_loc];
158159
} else if (remainder == 1) {
159160
h_val ^= SEED_TAB[(unsigned char)kmer_seq[k - 1] & CP_OFF];

‎recipes/indexlr.cpp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -248,7 +248,7 @@ main(int argc, char* argv[])
248248
out = fopen(outfile.c_str(), "w"); // NOLINT(android-cloexec-fopen)
249249
#endif
250250
}
251-
for (auto& infile : infiles) {
251+
for (const auto& infile : infiles) {
252252
std::unique_ptr<btllib::Indexlr> indexlr;
253253
if (with_repeat && with_solid) {
254254
flags |= btllib::Indexlr::Flag::FILTER_IN;

‎recipes/mi_bloom_filter.cpp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -247,7 +247,7 @@ main(int argc, char* argv[])
247247
for (int mi_bf_stage = 0; mi_bf_stage < 3; mi_bf_stage++) {
248248
btllib::log_info(stages[mi_bf_stage] + std::string(" stage started"));
249249

250-
for (auto& read_path : read_paths) {
250+
for (const auto& read_path : read_paths) {
251251
btllib::SeqReader reader(read_path,
252252
btllib::SeqReader::Flag::SHORT_MODE,
253253
DEFAULT_SEQ_READER_THREADS);

‎recipes/randseq.cpp‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -145,14 +145,15 @@ class Logger
145145
std::lround((double)generated_seqs / (double)total_seqs * 100.0);
146146
const double seq_ratio =
147147
((double)total_seqs - (double)generated_seqs) / (double)generated_seqs;
148-
const std::chrono::duration<double> total_elapsed = (current_time - start_time);
148+
const std::chrono::duration<double> total_elapsed =
149+
(current_time - start_time);
149150
auto remaining = std::lround(seq_ratio * total_elapsed.count() + 1);
150151
const std::string line = "[" + std::to_string(generated_seqs) + "/" +
151-
std::to_string(total_seqs) + "] Generated " +
152-
std::to_string(generated_bp) + unit + " @" +
153-
std::to_string(speed) + unit + "/s (" +
154-
std::to_string(progress) + "%, ~" +
155-
std::to_string(remaining) + "s remaining)";
152+
std::to_string(total_seqs) + "] Generated " +
153+
std::to_string(generated_bp) + unit + " @" +
154+
std::to_string(speed) + unit + "/s (" +
155+
std::to_string(progress) + "%, ~" +
156+
std::to_string(remaining) + "s remaining)";
156157
std::cerr << line << "\r";
157158
last_log = current_time;
158159
last_line_length = line.size();

‎src/btllib/nthash.cpp‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -273,7 +273,8 @@ parse_seeds(const std::vector<std::string>& seed_strings,
273273
}
274274
}
275275
const unsigned num_cares = care_blocks.size() * 2 + care_monos.size();
276-
const unsigned num_ignores = ignore_blocks.size() * 2 + ignore_monos.size() + 2;
276+
const unsigned num_ignores =
277+
ignore_blocks.size() * 2 + ignore_monos.size() + 2;
277278
if (num_ignores < num_cares) {
278279
unsigned string_end = seed_string.length();
279280
const std::array<unsigned, 2> block{ { 0, string_end } };

0 commit comments

Comments
 (0)