[med-svn] [Git][med-team/btllib][master] 6 commits: Exclude 32bit architectures since upstream confirmed these are not supported.
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Feb 2 07:13:36 GMT 2023
Andreas Tille pushed to branch master at Debian Med / btllib
Commits:
fbbed381 by Andreas Tille at 2023-02-02T08:10:05+01:00
Exclude 32bit architectures since upstream confirmed these are not supported.
- - - - -
04e2126c by Andreas Tille at 2023-02-02T08:10:24+01:00
New upstream version 1.4.10+dfsg
- - - - -
0dd6b782 by Andreas Tille at 2023-02-02T08:10:24+01:00
routine-update: New upstream version
- - - - -
a170e3c5 by Andreas Tille at 2023-02-02T08:10:25+01:00
Update upstream source from tag 'upstream/1.4.10+dfsg'
Update to upstream version '1.4.10+dfsg'
with Debian dir 1a75f5a0c21b285ba963fc81c1d6d769b3d69c7f
- - - - -
515b6f1a by Andreas Tille at 2023-02-02T08:10:25+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
73c804fa by Andreas Tille at 2023-02-02T08:12:03+01:00
routine-update: Ready to upload to unstable
- - - - -
19 changed files:
- + CITATION.cff
- README.md
- debian/changelog
- debian/control
- include/btllib/counting_bloom_filter.hpp
- include/btllib/mi_bloom_filter.hpp
- include/btllib/nthash.hpp
- include/btllib/seq_reader.hpp
- include/btllib/seq_reader_sam_module.hpp
- recipes/indexlr.cpp
- src/btllib/data_stream.cpp
- src/btllib/nthash.cpp
- src/btllib/nthash_lowlevel.cpp
- src/btllib/process_pipeline.cpp
- src/btllib/seq_reader.cpp
- src/btllib/seq_reader_gfa2_module.cpp
- src/btllib/seq_reader_sam_module.cpp
- src/btllib/seq_writer.cpp
- tests/nthash.cpp
Changes:
=====================================
CITATION.cff
=====================================
@@ -0,0 +1,59 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+ - family-names: "Nikolić"
+ given-names: "Vladimir"
+ orcid: "https://orcid.org/0000-0002-2992-9935"
+ - family-names: Kazemi
+ given-names: Parham
+ - family-names: Coombe
+ given-names: Lauren
+ orcid: "https://orcid.org/0000-0002-7518-2326"
+ - family-names: Wong
+ given-names: Johnathan
+ - family-names: Afshinfard
+ given-names: Amirhossein
+ orcid: "https://orcid.org/0000-0002-6875-4939"
+ - family-names: Chu
+ given-names: Justin
+ - family-names: Warren
+ given-names: René L.
+ orcid: "https://orcid.org/0000-0002-9890-2293"
+ - family-names: Birol
+ given-names: Inanç
+ orcid: "https://orcid.org/0000-0003-0950-7839"
+title: "btllib"
+url: "https://github.com/bcgsc/btllib"
+preferred-citation:
+ type: article
+ authors:
+ - family-names: "Nikolić"
+ given-names: "Vladimir"
+ orcid: "https://orcid.org/0000-0002-2992-9935"
+ - family-names: Kazemi
+ given-names: Parham
+ - family-names: Coombe
+ given-names: Lauren
+ orcid: "https://orcid.org/0000-0002-7518-2326"
+ - family-names: Wong
+ given-names: Johnathan
+ - family-names: Afshinfard
+ given-names: Amirhossein
+ orcid: "https://orcid.org/0000-0002-6875-4939"
+ - family-names: Chu
+ given-names: Justin
+ - family-names: Warren
+ given-names: René L.
+ orcid: "https://orcid.org/0000-0002-9890-2293"
+ - family-names: Birol
+ given-names: Inanç
+ orcid: "https://orcid.org/0000-0003-0950-7839"
+ doi: "10.21105/joss.04720"
+ url: "https://doi.org/10.21105/joss.04720"
+ year: 2022
+ publisher: "The Open Journal"
+ volume: 7
+ number: 79
+ pages: 4720
+ title: "btllib: A C++ library with Python interface for efficient genomic sequence processing"
+ journal: "Journal of Open Source Software"
=====================================
README.md
=====================================
@@ -3,6 +3,7 @@
[](https://lgtm.com/projects/g/bcgsc/btllib/context:cpp)
[](https://lgtm.com/projects/g/bcgsc/btllib/alerts/)
[](https://dev.azure.com/bcgsc/btl_public/_build/latest?definitionId=1)
+[](https://doi.org/10.21105/joss.04720)
[Bioinformatics Technology Lab](http://www.birollab.ca/) common code library in C++ with Python wrappers.
@@ -82,5 +83,12 @@ Credits
- Components:
- [Hamid Mohamadi](https://github.com/mohamadi) and [Parham Kazemi](https://github.com/parham-k) for [ntHash](https://github.com/bcgsc/ntHash)
- [Justin Chu](https://github.com/JustinChu) for [MIBloomFilter](https://github.com/bcgsc/btl_bloomfilter)
+- Included dependencies:
- [Chase Geigle](https://github.com/skystrife) for [cpptoml](https://github.com/skystrife/cpptoml)
- Simon Gog, Timo Beller, Alistair Moffat, and Matthias Petri for [sdsl-lite](https://github.com/simongog/sdsl-lite)
+
+Citing
+---
+If you use btllib in your research, please cite:
+
+Nikolić et al., (2022). btllib: A C++ library with Python interface for efficient genomic sequence processing. Journal of Open Source Software, 7(79), 4720, https://doi.org/10.21105/joss.04720
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+btllib (1.4.10+dfsg-1) unstable; urgency=medium
+
+ * Exclude 32bit architectures since upstream confirmed these are not
+ supported.
+ Closes: #1022772
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Thu, 02 Feb 2023 08:10:47 +0100
+
btllib (1.4.9+dfsg-2) unstable; urgency=medium
* Packaging update
=====================================
debian/control
=====================================
@@ -11,14 +11,14 @@ Build-Depends: debhelper-compat (= 13),
# libsdsl-dev, # only mentioned in doc but package builds without this as well
libomp-dev,
samtools
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/btllib
Vcs-Git: https://salsa.debian.org/med-team/btllib.git
Homepage: https://github.com/bcgsc/btllib
Rules-Requires-Root: no
Package: libbtllib-dev
-Architecture: any
+Architecture: any-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
=====================================
include/btllib/counting_bloom_filter.hpp
=====================================
@@ -695,8 +695,11 @@ CountingBloomFilter<T>::insert(const uint64_t* hashes, T min_val)
update_done = array[hashes[i] % array_size].compare_exchange_strong(
tmp_min_val, new_val);
}
- if (update_done ||
- (min_val = contains(hashes)) == std::numeric_limits<T>::max()) {
+ if (update_done) {
+ break;
+ }
+ min_val = contains(hashes);
+ if (min_val == std::numeric_limits<T>::max()) {
break;
}
}
@@ -1005,4 +1008,4 @@ KmerCountingBloomFilter<T>::save(const std::string& path)
} // namespace btllib
-#endif
\ No newline at end of file
+#endif
=====================================
include/btllib/mi_bloom_filter.hpp
=====================================
@@ -84,9 +84,9 @@ public:
unsigned colli_count = 0;
for (unsigned i = 0; i < hash_num; ++i) {
const int magic = 0x3f;
- uint64_t pos = hash_values[i] % bv.size();
+ const uint64_t pos = hash_values[i] % bv.size();
uint64_t* data_index = bv.data() + (pos >> 6); // NOLINT
- uint64_t bit_mask_value = (uint64_t)1 << (pos & magic);
+ const uint64_t bit_mask_value = (uint64_t)1 << (pos & magic);
colli_count +=
__sync_fetch_and_or(data_index, bit_mask_value) >> (pos & magic) & 1;
}
@@ -208,7 +208,7 @@ public:
log_info("MIBloomFilter: Loading data vector");
- long int l_cur_pos = ftell(file);
+ const long int l_cur_pos = ftell(file);
auto ret = fseek(file, 0, 2);
check_error(ret != 0,
"MIBloomFilter: Failed to seek to end of file: " +
@@ -233,7 +233,7 @@ public:
}
else {
- std::string bv_filename = filter_file_path + ".sdsl";
+ const std::string bv_filename = filter_file_path + ".sdsl";
log_info("MIBloomFilter: Loading sdsl interleaved bit vector from: " +
bv_filename);
load_from_file(m_bv, bv_filename);
@@ -280,7 +280,7 @@ public:
"MIBloomFilter: " + filter_file_path +
" could not be read.");
} else {
- std::string bv_filename = filter_file_path + ".sdsl";
+ const std::string bv_filename = filter_file_path + ".sdsl";
// std::cerr << "Storing sdsl interleaved
// bit
// vector to: " << bv_filename
=====================================
include/btllib/nthash.hpp
=====================================
@@ -674,10 +674,14 @@ BTLLIB_NTHASH_PEEK(
peek(),
{
- std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> forward_hash_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> reverse_hash_tmp(new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> forward_hash_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> reverse_hash_tmp(
+ new uint64_t[blocks.size()]);
std::memcpy(fh_no_monomers_tmp.get(),
forward_hash.get(),
blocks.size() * sizeof(uint64_t));
@@ -708,10 +712,14 @@ BTLLIB_NTHASH_PEEK(
peek(char char_in),
{
- std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> forward_hash_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> reverse_hash_tmp(new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> forward_hash_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> reverse_hash_tmp(
+ new uint64_t[blocks.size()]);
std::memcpy(fh_no_monomers_tmp.get(),
forward_hash.get(),
blocks.size() * sizeof(uint64_t));
@@ -743,10 +751,14 @@ BTLLIB_NTHASH_PEEK(
peek_back(),
{
- std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> forward_hash_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> reverse_hash_tmp(new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> forward_hash_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> reverse_hash_tmp(
+ new uint64_t[blocks.size()]);
std::memcpy(fh_no_monomers_tmp.get(),
forward_hash.get(),
blocks.size() * sizeof(uint64_t));
@@ -777,10 +789,14 @@ BTLLIB_NTHASH_PEEK(
peek_back(char char_in),
{
- std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> forward_hash_tmp(new uint64_t[blocks.size()]);
- std::unique_ptr<uint64_t[]> reverse_hash_tmp(new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> fh_no_monomers_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> rh_no_monomers_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> forward_hash_tmp(
+ new uint64_t[blocks.size()]);
+ const std::unique_ptr<uint64_t[]> reverse_hash_tmp(
+ new uint64_t[blocks.size()]);
std::memcpy(fh_no_monomers_tmp.get(),
forward_hash.get(),
blocks.size() * sizeof(uint64_t));
@@ -815,4 +831,4 @@ BTLLIB_NTHASH_PEEK(
} // namespace btllib
-#endif
\ No newline at end of file
+#endif
=====================================
include/btllib/seq_reader.hpp
=====================================
@@ -311,7 +311,7 @@ SeqReader::read_transition(Module& module,
if (!reader_record->seq.empty()) {
update_cstring_records(records, counter);
}
- } else if (!reader_record->seq.empty()) {
+ } else if (reader_record != nullptr && !reader_record->seq.empty()) {
update_cstring_records(records, counter);
}
}
@@ -334,4 +334,4 @@ SeqReader::read_from_file(Module& module,
} // namespace btllib
-#endif
\ No newline at end of file
+#endif
=====================================
include/btllib/seq_reader_sam_module.hpp
=====================================
@@ -25,6 +25,13 @@ private:
ALIGNMENTS
};
+ ~SeqReaderSamModule()
+ {
+ if (loader_thread) {
+ loader_thread->join();
+ }
+ }
+
std::unique_ptr<ProcessPipeline> samtools_process;
std::unique_ptr<std::thread> loader_thread;
CString tmp;
@@ -46,7 +53,8 @@ SeqReaderSamModule::read_buffer(ReaderType& reader, RecordType& record)
(void)reader;
(void)record;
{
- ProcessPipeline version_test("samtools --version 2>/dev/stdout | head -n2");
+ const ProcessPipeline version_test(
+ "samtools --version 2>/dev/stdout | head -n2");
char* line = nullptr;
size_t n = 0;
std::string version = "\n";
@@ -92,7 +100,6 @@ SeqReaderSamModule::read_buffer(ReaderType& reader, RecordType& record)
}
samtools_process->close_in();
}));
- loader_thread->detach();
return false;
}
=====================================
recipes/indexlr.cpp
=====================================
@@ -164,7 +164,7 @@ main(int argc, char* argv[])
" threads does not scale, reverting to 5.\n")
<< std::flush;
}
- std::vector<std::string> infiles(&argv[optind], &argv[argc]);
+ const std::vector<std::string> infiles(&argv[optind], &argv[argc]);
if (argc < 2) {
print_usage();
std::exit(EXIT_FAILURE); // NOLINT(concurrency-mt-unsafe)
@@ -226,7 +226,7 @@ main(int argc, char* argv[])
out = fopen(outfile.c_str(), "w"); // NOLINT(android-cloexec-fopen)
#endif
}
- for (auto& infile : infiles) {
+ for (const auto& infile : infiles) {
std::unique_ptr<btllib::Indexlr> indexlr;
if (with_repeat && with_solid) {
flags |= btllib::Indexlr::Flag::FILTER_IN;
@@ -305,7 +305,7 @@ main(int argc, char* argv[])
}
}
{
- std::unique_lock<std::mutex> lock(output_queue_mutex);
+ const std::unique_lock<std::mutex> lock(output_queue_mutex);
if (!ss.str().empty()) {
output_queue.push(ss.str());
}
=====================================
src/btllib/data_stream.cpp
=====================================
@@ -12,6 +12,7 @@
#include <cstring>
#include <map>
#include <memory>
+#include <sstream>
#include <string>
#include <vector>
@@ -133,7 +134,7 @@ get_datatype_cmd(const std::string& path,
for (const auto& existence_cmd : datatype.cmds_check_existence) {
const pid_t pid = fork();
if (pid == 0) {
- int null_fd = open("/dev/null", O_WRONLY, 0);
+ const int null_fd = open("/dev/null", O_WRONLY, 0);
dup2(null_fd, STDOUT_FILENO);
dup2(null_fd, STDERR_FILENO);
close(null_fd);
@@ -238,13 +239,13 @@ peel_datatype(const std::string& path, DataStream::Operation op)
}
static std::string
-form_string_cmd(std::vector<std::string>& cmd_layers,
- DataStream::Operation op,
+form_string_cmd(const std::vector<std::string>& cmd_layers,
+ const DataStream::Operation op,
const std::string& path)
{
- std::string result_cmd;
+ std::stringstream result_cmd_ss;
for (size_t i = 0; i < cmd_layers.size(); i++) {
- auto& cmd = cmd_layers[i];
+ std::string cmd = cmd_layers[i];
if (op == DataStream::Operation::WRITE ||
op == DataStream::Operation::APPEND) {
if (i == cmd_layers.size() - 1) {
@@ -278,10 +279,11 @@ form_string_cmd(std::vector<std::string>& cmd_layers,
}
}
if (i > 0) {
- result_cmd += " | ";
+ result_cmd_ss << " | ";
}
- result_cmd += cmd;
+ result_cmd_ss << cmd;
}
+ std::string result_cmd = result_cmd_ss.str();
check_error(result_cmd.empty(),
(op == DataStream::Operation::READ ? "Error loading from "
=====================================
src/btllib/nthash.cpp
=====================================
@@ -211,7 +211,7 @@ check_seeds(const std::vector<std::string>& seeds, unsigned k)
check_error(seed.length() != k,
"Spaced seed string length (" + std::to_string(seed.length()) +
") not equal to k=" + std::to_string(k) + " in " + seed);
- std::string reversed(seed.rbegin(), seed.rend());
+ const std::string reversed(seed.rbegin(), seed.rend());
check_warning(
seed != reversed,
"Seed " + seed +
@@ -243,7 +243,7 @@ parse_seeds(const std::vector<std::string>& seed_strings,
std::vector<SpacedSeedMonomers>& out_monomers)
{
for (const auto& seed_string : seed_strings) {
- char pad = seed_string[seed_string.length() - 1] == '1' ? '0' : '1';
+ const char pad = seed_string[seed_string.length() - 1] == '1' ? '0' : '1';
const std::string padded_string = seed_string + pad;
SpacedSeedBlocks care_blocks, ignore_blocks;
std::vector<unsigned> care_monos, ignore_monos;
@@ -254,7 +254,7 @@ parse_seeds(const std::vector<std::string>& seed_strings,
if (pos - i_start == 1) {
care_monos.push_back(i_start);
} else {
- std::array<unsigned, 2> block{ { i_start, pos } };
+ const std::array<unsigned, 2> block{ { i_start, pos } };
care_blocks.push_back(block);
}
i_start = pos;
@@ -263,18 +263,19 @@ parse_seeds(const std::vector<std::string>& seed_strings,
if (pos - i_start == 1) {
ignore_monos.push_back(i_start);
} else {
- std::array<unsigned, 2> block{ { i_start, pos } };
+ const std::array<unsigned, 2> block{ { i_start, pos } };
ignore_blocks.push_back(block);
}
i_start = pos;
is_care_block = true;
}
}
- unsigned num_cares = care_blocks.size() * 2 + care_monos.size();
- unsigned num_ignores = ignore_blocks.size() * 2 + ignore_monos.size() + 2;
+ const unsigned num_cares = care_blocks.size() * 2 + care_monos.size();
+ const unsigned num_ignores =
+ ignore_blocks.size() * 2 + ignore_monos.size() + 2;
if (num_ignores < num_cares) {
unsigned string_end = seed_string.length();
- std::array<unsigned, 2> block{ { 0, string_end } };
+ const std::array<unsigned, 2> block{ { 0, string_end } };
ignore_blocks.push_back(block);
out_blocks.push_back(ignore_blocks);
out_monomers.push_back(ignore_monos);
@@ -330,4 +331,4 @@ BlindNtHash::sub(const std::vector<unsigned>& positions,
hashes_array.get());
}
-} // namespace btllib
\ No newline at end of file
+} // namespace btllib
=====================================
src/btllib/nthash_lowlevel.cpp
=====================================
@@ -8,25 +8,25 @@ ntf64(const char* kmer_seq, const unsigned k)
uint64_t h_val = 0;
for (unsigned i = 0; i < k / 4; i++) {
h_val = srol(h_val, 4);
- uint8_t curr_offset = 4 * i;
- uint8_t tetramer_loc =
+ const uint8_t curr_offset = 4 * i;
+ const uint8_t tetramer_loc =
64 * CONVERT_TAB[(unsigned char)kmer_seq[curr_offset]] + // NOLINT
16 * CONVERT_TAB[(unsigned char)kmer_seq[curr_offset + 1]] + // NOLINT
4 * CONVERT_TAB[(unsigned char)kmer_seq[curr_offset + 2]] +
CONVERT_TAB[(unsigned char)kmer_seq[curr_offset + 3]];
h_val ^= TETRAMER_TAB[tetramer_loc];
}
- unsigned remainder = k % 4;
+ const unsigned remainder = k % 4;
h_val = srol(h_val, remainder);
if (remainder == 3) {
- uint8_t trimer_loc =
+ const uint8_t trimer_loc =
16 * CONVERT_TAB[(unsigned char)kmer_seq[k - 3]] + // NOLINT
4 * CONVERT_TAB[(unsigned char)kmer_seq[k - 2]] +
CONVERT_TAB[(unsigned char)kmer_seq[k - 1]];
h_val ^= TRIMER_TAB[trimer_loc];
} else if (remainder == 2) {
- uint8_t dimer_loc = 4 * CONVERT_TAB[(unsigned char)kmer_seq[k - 2]] +
- CONVERT_TAB[(unsigned char)kmer_seq[k - 1]];
+ const uint8_t dimer_loc = 4 * CONVERT_TAB[(unsigned char)kmer_seq[k - 2]] +
+ CONVERT_TAB[(unsigned char)kmer_seq[k - 1]];
h_val ^= DIMER_TAB[dimer_loc];
} else if (remainder == 1) {
h_val ^= SEED_TAB[(unsigned char)kmer_seq[k - 1]];
@@ -38,24 +38,25 @@ uint64_t
ntr64(const char* kmer_seq, const unsigned k)
{
uint64_t h_val = 0;
- unsigned remainder = k % 4;
+ const unsigned remainder = k % 4;
if (remainder == 3) {
- uint8_t trimer_loc =
+ const uint8_t trimer_loc =
16 * RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 1]] + // NOLINT
4 * RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 2]] +
RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 3]];
h_val ^= TRIMER_TAB[trimer_loc];
} else if (remainder == 2) {
- uint8_t dimer_loc = 4 * RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 1]] +
- RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 2]];
+ const uint8_t dimer_loc =
+ 4 * RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 1]] +
+ RC_CONVERT_TAB[(unsigned char)kmer_seq[k - 2]];
h_val ^= DIMER_TAB[dimer_loc];
} else if (remainder == 1) {
h_val ^= SEED_TAB[(unsigned char)kmer_seq[k - 1] & CP_OFF];
}
for (unsigned i = 0; i < k / 4; i++) {
h_val = srol(h_val, 4);
- uint8_t curr_offset = 4 * (k / 4 - i) - 1;
- uint8_t tetramer_loc =
+ const uint8_t curr_offset = 4 * (k / 4 - i) - 1;
+ const uint8_t tetramer_loc =
64 * RC_CONVERT_TAB[(unsigned char)kmer_seq[curr_offset]] + // NOLINT
16 * RC_CONVERT_TAB[(unsigned char)kmer_seq[curr_offset - 1]] + // NOLINT
4 * RC_CONVERT_TAB[(unsigned char)kmer_seq[curr_offset - 2]] +
@@ -178,7 +179,7 @@ ntmc64(const char* kmer_seq,
const unsigned m,
uint64_t* h_val)
{
- uint64_t b_val = ntc64(kmer_seq, k);
+ const uint64_t b_val = ntc64(kmer_seq, k);
nte64(b_val, k, m, h_val);
}
@@ -190,7 +191,7 @@ ntmc64(const char* kmer_seq,
uint64_t& rh_val,
uint64_t* h_val)
{
- uint64_t b_val = ntc64(kmer_seq, k, fh_val, rh_val);
+ const uint64_t b_val = ntc64(kmer_seq, k, fh_val, rh_val);
nte64(b_val, k, m, h_val);
}
@@ -203,7 +204,7 @@ ntmc64(const unsigned char char_out,
uint64_t& rh_val,
uint64_t* h_val)
{
- uint64_t b_val = ntc64(char_out, char_in, k, fh_val, rh_val);
+ const uint64_t b_val = ntc64(char_out, char_in, k, fh_val, rh_val);
nte64(b_val, k, m, h_val);
}
@@ -216,7 +217,7 @@ ntmc64l(const unsigned char char_out,
uint64_t& rh_val,
uint64_t* h_val)
{
- uint64_t b_val = ntc64l(char_out, char_in, k, fh_val, rh_val);
+ const uint64_t b_val = ntc64l(char_out, char_in, k, fh_val, rh_val);
nte64(b_val, k, m, h_val);
}
@@ -359,7 +360,7 @@ ntmc64(const unsigned char char_out,
uint64_t* h_val,
bool& h_stn)
{
- uint64_t b_val = ntc64(char_out, char_in, k, fh_val, rh_val);
+ const uint64_t b_val = ntc64(char_out, char_in, k, fh_val, rh_val);
h_stn = rh_val < fh_val;
nte64(b_val, k, m, h_val);
}
@@ -440,7 +441,7 @@ ntmsm64(const char* kmer_seq,
}
fh_nomonos[i_seed] = fh_seed;
rh_nomonos[i_seed] = rh_seed;
- for (unsigned pos : seeds_monomers[i_seed]) {
+ for (const unsigned pos : seeds_monomers[i_seed]) {
fh_seed ^= MS_TAB((unsigned char)kmer_seq[pos], k - 1 - pos);
rh_seed ^= MS_TAB((unsigned char)kmer_seq[pos] & CP_OFF, pos);
}
@@ -548,4 +549,4 @@ ntmsm64l(const char* kmer_seq,
, fh_seed = sror(fh_seed);)
}
-} // namespace btllib
\ No newline at end of file
+} // namespace btllib
=====================================
src/btllib/process_pipeline.cpp
=====================================
@@ -805,7 +805,7 @@ process_spawner_init()
ProcessPipeline::ProcessPipeline(const std::string& cmd)
{
- std::unique_lock<std::mutex> lock(process_spawner_comm_mutex);
+ const std::unique_lock<std::mutex> lock(process_spawner_comm_mutex);
const auto op = PipelineOperation::RUN;
check_error(!write_to_spawner(&op, sizeof(op)),
@@ -903,7 +903,7 @@ ProcessPipeline::end()
close_in();
close_out();
- std::unique_lock<std::mutex> lock(process_spawner_comm_mutex);
+ const std::unique_lock<std::mutex> lock(process_spawner_comm_mutex);
const auto op = PipelineOperation::END;
check_error(!write_to_spawner(&op, sizeof(op)) ||
=====================================
src/btllib/seq_reader.cpp
=====================================
@@ -97,7 +97,7 @@ bool
SeqReader::load_buffer()
{
buffer.start = 0;
- char last = buffer.end > 0 ? buffer.data[buffer.end - 1] : char(0);
+ const char last = buffer.end > 0 ? buffer.data[buffer.end - 1] : char(0);
buffer.end = 0;
do {
buffer.end += fread(buffer.data.data() + buffer.end,
@@ -224,7 +224,7 @@ void
SeqReader::determine_format()
{
load_buffer();
- bool empty = buffer.end - buffer.start == 1;
+ const bool empty = buffer.end - buffer.start == 1;
check_warning(empty, std::string(source_path) + " is empty.");
if (empty) {
@@ -254,7 +254,7 @@ SeqReader::start_reader()
{
reader_thread = std::unique_ptr<std::thread>(new std::thread([this]() {
{
- std::unique_lock<std::mutex> lock(format_mutex);
+ const std::unique_lock<std::mutex> lock(format_mutex);
determine_format();
format_cv.notify_all();
}
@@ -330,10 +330,11 @@ SeqReader::start_processors()
break;
}
}
- size_t id_start = (format == Format::FASTA ||
- format == Format::FASTQ || format == Format::SAM)
- ? 1
- : 0;
+ const size_t id_start =
+ (format == Format::FASTA || format == Format::FASTQ ||
+ format == Format::SAM)
+ ? 1
+ : 0;
switch (format) {
case Format::FASTA:
@@ -400,7 +401,7 @@ SeqReader::start_processors()
}
if (fold_case()) {
for (auto& c : seq) {
- char old = c;
+ const char old = c;
c = CAPITALS[(unsigned char)(c)];
if (!bool(c)) {
log_error(std::string("A sequence contains invalid "
@@ -463,4 +464,4 @@ SeqReader::read_block()
return block;
}
-} // namespace btllib
\ No newline at end of file
+} // namespace btllib
=====================================
src/btllib/seq_reader_gfa2_module.cpp
=====================================
@@ -18,7 +18,7 @@ SeqReaderGfa2Module::buffer_valid(const char* buffer, const size_t size)
auto is_a_spec = [&](unsigned char c) {
bool found = false;
- for (unsigned char spec : specs) {
+ for (const unsigned char spec : specs) {
if (c == spec) {
found = true;
break;
@@ -70,4 +70,4 @@ SeqReaderGfa2Module::buffer_valid(const char* buffer, const size_t size)
return has_id;
}
-} // namespace btllib
\ No newline at end of file
+} // namespace btllib
=====================================
src/btllib/seq_reader_sam_module.cpp
=====================================
@@ -93,7 +93,7 @@ SeqReaderSamModule::buffer_valid(const char* buffer, const size_t size)
}
break;
case TLEN:
- if (!(bool(std::isdigit(c)) || c == '-')) {
+ if (!bool(std::isdigit(c)) && c != '-') {
return false;
}
break;
=====================================
src/btllib/seq_writer.cpp
=====================================
@@ -67,11 +67,11 @@ SeqWriter::write(const std::string& id,
}
{
- std::unique_lock<std::mutex> lock(mutex);
+ const std::unique_lock<std::mutex> lock(mutex);
if (fwrite(output.c_str(), 1, output.size(), sink) != output.size()) {
log_error("SeqWriter: fwrite failed: " + get_strerror());
}
}
}
-} // namespace btllib
\ No newline at end of file
+} // namespace btllib
=====================================
tests/nthash.cpp
=====================================
@@ -465,11 +465,16 @@ main()
btllib::SeedNtHash nthash1(seq_fwd, seeds, h, seeds[0].length());
btllib::SeedNtHash nthash2(seq_rev, seeds, h, seeds[0].length());
+
+ bool r1 = nthash1.roll();
+ bool r2 = nthash2.roll();
- while (nthash1.roll() & nthash2.roll()) {
+ while (r1 && r2) {
TEST_ASSERT_ARRAY_EQ(nthash1.hashes(), nthash2.hashes(), h);
+ r1 = nthash1.roll();
+ r2 = nthash2.roll();
}
}
return 0;
-}
\ No newline at end of file
+}
View it on GitLab: https://salsa.debian.org/med-team/btllib/-/compare/8fd69c043b914972f4df42174085055eb8b23720...73c804fa28afeeaa8c0034fdd510559d9ac473d2
--
View it on GitLab: https://salsa.debian.org/med-team/btllib/-/compare/8fd69c043b914972f4df42174085055eb8b23720...73c804fa28afeeaa8c0034fdd510559d9ac473d2
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