From 65542209ac8b5cf7415567229db797293324083a Mon Sep 17 00:00:00 2001 From: Benjamin Buchfink Date: Thu, 16 Jan 2025 21:03:17 +0100 Subject: [PATCH] Squashed commit of the following: commit 181c38bdb8db8a246cda8556657afe0eaa0e8f8b Author: Benjamin Buchfink Date: Thu Jan 16 21:02:14 2025 +0100 fixed gcc 4.8 errors commit dde4eaae949a8fb56622f1c349d458e8c729470c Author: Benjamin Buchfink Date: Thu Jan 16 21:01:34 2025 +0100 fixed gcc 4.8 errors commit d551387743d9bbee80cf5a45714a580f61228361 Author: Benjamin Buchfink Date: Thu Jan 16 21:00:36 2025 +0100 fixed gcc 4.8 errors commit 0e4dc1ee12f9216cb0ef263491e3afbbe23747f2 Author: Benjamin Buchfink Date: Thu Jan 16 20:59:19 2025 +0100 fixed gcc 4.8 errors commit 1f0cfd8a2f18200af09b0e57246682b6bec755c3 Author: Benjamin Buchfink Date: Thu Jan 16 20:58:05 2025 +0100 fixed gcc 4.8 errors commit f59c5e02a17a5124237585354b21e07f37d3a074 Author: Benjamin Buchfink Date: Thu Jan 16 20:56:08 2025 +0100 Fixed gcc 4.8 errors --- src/basic/config.cpp | 8 ++++---- src/cluster/external/make_seed_table.cpp | 2 +- src/cluster/helpers.cpp | 2 +- src/data/index.cpp | 2 +- src/search/setup.cpp | 4 ++-- src/util/io/output_stream_buffer.h | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/basic/config.cpp b/src/basic/config.cpp index a336352c..7aa9eb3e 100644 --- a/src/basic/config.cpp +++ b/src/basic/config.cpp @@ -111,7 +111,7 @@ pair 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) @@ -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); @@ -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) @@ -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) diff --git a/src/cluster/external/make_seed_table.cpp b/src/cluster/external/make_seed_table.cpp index 14cfa10b..cb825126 100644 --- a/src/cluster/external/make_seed_table.cpp +++ b/src/cluster/external/make_seed_table.cpp @@ -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; diff --git a/src/cluster/helpers.cpp b/src/cluster/helpers.cpp index b0e086b3..581659b5 100644 --- a/src/cluster/helpers.cpp +++ b/src/cluster/helpers.cpp @@ -91,7 +91,7 @@ vector 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(); diff --git a/src/data/index.cpp b/src/data/index.cpp index 4fb988f1..95b3ad5a 100644 --- a/src/data/index.cpp +++ b/src/data/index.cpp @@ -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); diff --git a/src/search/setup.cpp b/src/search/setup.cpp index d8c2bf80..5b898ef7 100644 --- a/src/search/setup.cpp +++ b/src/search/setup.cpp @@ -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) { diff --git a/src/util/io/output_stream_buffer.h b/src/util/io/output_stream_buffer.h index 94194085..182daeb6 100644 --- a/src/util/io/output_stream_buffer.h +++ b/src/util/io/output_stream_buffer.h @@ -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 buf_; }; \ No newline at end of file