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commit 181c38bdb8db8a246cda8556657afe0eaa0e8f8b
Author: Benjamin Buchfink <buchfink@gmail.com>
Date:   Thu Jan 16 21:02:14 2025 +0100

    fixed gcc 4.8 errors

commit dde4eaae949a8fb56622f1c349d458e8c729470c
Author: Benjamin Buchfink <buchfink@gmail.com>
Date:   Thu Jan 16 21:01:34 2025 +0100

    fixed gcc 4.8 errors

commit d551387743d9bbee80cf5a45714a580f61228361
Author: Benjamin Buchfink <buchfink@gmail.com>
Date:   Thu Jan 16 21:00:36 2025 +0100

    fixed gcc 4.8 errors

commit 0e4dc1ee12f9216cb0ef263491e3afbbe23747f2
Author: Benjamin Buchfink <buchfink@gmail.com>
Date:   Thu Jan 16 20:59:19 2025 +0100

    fixed gcc 4.8 errors

commit 1f0cfd8a2f18200af09b0e57246682b6bec755c3
Author: Benjamin Buchfink <buchfink@gmail.com>
Date:   Thu Jan 16 20:58:05 2025 +0100

    fixed gcc 4.8 errors

commit f59c5e02a17a5124237585354b21e07f37d3a074
Author: Benjamin Buchfink <buchfink@gmail.com>
Date:   Thu Jan 16 20:56:08 2025 +0100

    Fixed gcc 4.8 errors
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bbuchfink committed Jan 16, 2025
1 parent 711f910 commit 6554220
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Showing 6 changed files with 10 additions and 10 deletions.
8 changes: 4 additions & 4 deletions src/basic/config.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ pair<double, int> block_size(int64_t memory_limit, int64_t db_letters, Sensitivi
const double hash_join_factor = 1.0 + (double)thread_count / (seedp_count(Search::seedp_bits(shape_weight, thread_count, c)) / c);
const double seed_array_entry_size = 18.0 * hash_join_factor;
b = m / (seed_array_entry_size * seeds_per_letter + 2.0);
} while ((int64_t)b * 1'000'000'000 < db_letters && b < max_b && c < max_c);
} while ((int64_t)b * 1000000000 < db_letters && b < max_b && c < max_c);
/*if (b > 4)
b = floor(b);
else if (b > 0.4)
Expand Down Expand Up @@ -410,7 +410,7 @@ Config::Config(int argc, const char **argv, bool check_io, CommandLineParser& pa

auto& advanced_gen = parser.add_group("Advanced/general", { blastp, blastx, blastn, CLUSTER_REASSIGN, regression_test, cluster, DEEPCLUST, LINCLUST, makedb });
advanced_gen.add()
("file-buffer-size", 0, "file buffer size in bytes (default=67108864)", file_buffer_size, INT64_C(67'108'864))
("file-buffer-size", 0, "file buffer size in bytes (default=67108864)", file_buffer_size, INT64_C(67108864))
("no-unlink", 0, "Do not unlink temporary files.", no_unlink)
("ignore-warnings", 0, "Ignore warnings", ignore_warnings)
("no-parse-seqids", 0, "Print raw seqids without parsing", no_parse_seqids);
Expand Down Expand Up @@ -440,7 +440,7 @@ Config::Config(int argc, const char **argv, bool check_io, CommandLineParser& pa
("ungapped-evalue-short", 0, "E-value threshold for ungapped filter (short reads) (auto)", ungapped_evalue_short_, -1.0)
("gapped-filter-evalue", 0, "E-value threshold for gapped filter (auto)", gapped_filter_evalue_, -1.0)
("band", 0, "band for dynamic programming computation", padding)
("swipe-task-size", 0, "task size for DP parallelism (100000000)", swipe_task_size, INT64_C(100'000'000))
("swipe-task-size", 0, "task size for DP parallelism (100000000)", swipe_task_size, INT64_C(100000000))
("shape-mask", 0, "seed shapes", shape_mask)
("multiprocessing", 0, "enable distributed-memory parallel processing", multiprocessing)
("mp-init", 0, "initialize multiprocessing run", mp_init)
Expand Down Expand Up @@ -610,7 +610,7 @@ Config::Config(int argc, const char **argv, bool check_io, CommandLineParser& pa
("deque_bucket_size", 0, "", deque_bucket_size, (size_t)524288)
("query-match-distance-threshold", 0, "", query_match_distance_threshold, -1.0)
("length-ratio-threshold", 0, "", length_ratio_threshold, -1.0)
("max-swipe-dp", 0, "", max_swipe_dp, INT64_C(1'000'000))
("max-swipe-dp", 0, "", max_swipe_dp, INT64_C(1000000))
("no-reextend", 0, "", no_reextend)
("no-reorder", 0, "", no_reorder)
("file1", 0, "", file1)
Expand Down
2 changes: 1 addition & 1 deletion src/cluster/external/make_seed_table.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ struct SeedCallback {
};

void make_seed_table() {
static const int64_t BLOCK_SIZE = 1'000'000'000;
static const int64_t BLOCK_SIZE = 1000000000;
config.database.require();
const Sensitivity sens = Sensitivity::FASTER;

Expand Down
2 changes: 1 addition & 1 deletion src/cluster/helpers.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ vector<Int> read(const string& file_name, const SequenceFile& db) {
const auto member_oid = db.accession_to_oid(member);
v[member_oid.front()] = (Int)centroid_oid.front();
++mappings;
if (mappings % 1'000'000 == 0)
if (mappings % 1000000 == 0)
log_stream << "#Entries: " << mappings << endl;
}
in.close();
Expand Down
2 changes: 1 addition & 1 deletion src/data/index.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
#include "util/log_stream.h"

void makeindex() {
static const size_t MAX_LETTERS = 100'000'000;
static const size_t MAX_LETTERS = 100000000;
if (config.database.empty())
throw std::runtime_error("Missing parameter: database file (--db/-d).");
DatabaseFile db(config.database);
Expand Down
4 changes: 2 additions & 2 deletions src/search/setup.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -289,10 +289,10 @@ bool use_single_indexed(double coverage, size_t query_letters, size_t ref_letter
if (coverage >= SINGLE_INDEXED_SEED_SPACE_MAX_COVERAGE)
return false;
if (config.sensitivity >= Sensitivity::SENSITIVE) {
return query_letters < 300'000llu && query_letters * 20'000llu < ref_letters;
return query_letters < 300000llu && query_letters * 20000llu < ref_letters;
}
else
return query_letters < 3'000'000llu && query_letters * 2'000llu < ref_letters;
return query_letters < 3000000llu && query_letters * 2000llu < ref_letters;
}

bool keep_target_id(const Search::Config& cfg) {
Expand Down
2 changes: 1 addition & 1 deletion src/util/io/output_stream_buffer.h
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ struct OutputStreamBuffer : public StreamEntity
virtual int64_t tell() override;
private:

static const size_t STDOUT_BUF_SIZE = 4'096;
static const size_t STDOUT_BUF_SIZE = 4096;
const size_t buf_size_;
std::unique_ptr<char[]> buf_;
};

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