squash commit for v2.1.24

Author: bbuchfink

CITATION.cff

@@ -13,4 +13,4 @@ date-released: 2021-04-07
 doi: "10.1038/s41592-021-01101-x"
 message: "If you use this software, please cite it using these metadata."
 title: "Sensitive protein alignments at tree-of-life scale using DIAMOND"
-version: "2.1.22"
+version: "2.1.24"

CMakeLists.txt

@@ -409,12 +409,12 @@ set(OBJECTS
         src/util/tsv/join.cpp
         src/dp/scalar/smith_waterman.cpp
         src/tools/tsv.cpp
-        #src/cluster/external/external.cpp
-        #src/cluster/external/seed_table.cpp
-        #src/cluster/external/pair_table.cpp
-        #src/cluster/external/align.cpp
-        #src/cluster/external/cluster.cpp
-        #src/cluster/external/output.cpp
+        src/cluster/external/external.cpp
+        src/cluster/external/seed_table.cpp
+        src/cluster/external/pair_table.cpp
+        src/cluster/external/align.cpp
+        src/cluster/external/cluster.cpp
+        src/cluster/external/output.cpp
         #src/util/algo/mcl.cpp
         #src/stats/blast/matrix_adjust.cpp
         src/stats/blast/ncbi.cpp

src/align/global_ranking/extend.cpp

@@ -95,7 +95,7 @@ void extend(SequenceFile& db, TempFile& merged_query_list, BitVector& ranking_db
 	InputFile query_list(merged_query_list);
 	db.set_seqinfo_ptr(0);
 	db.flags() |= SequenceFile::Flags::SEQS;
-	cfg.target.reset(db.load_seqs(INT64_MAX, &ranking_db_filter));
+	cfg.target.reset(db.load_seqs(INT64_MAX, 0, &ranking_db_filter));
 	TargetMap db2block_id;
 	const BlockId db_count = cfg.target->seqs().size();
 	db2block_id.reserve(db_count);
@@ -187,7 +187,7 @@ void extend(Search::Config& cfg, Consumer& out) {
 		cfg.db->flags() |= SequenceFile::Flags::TITLES;
 	if (bool(cfg.output_format->flags & Output::Flags::FULL_TITLES))
 		cfg.db->flags() |= SequenceFile::Flags::FULL_TITLES;
-	cfg.target.reset(cfg.db->load_seqs(INT64_MAX, &filter));
+	cfg.target.reset(cfg.db->load_seqs(INT64_MAX, 0, &filter));
 	TargetMap db2block_id;
 	const BlockId db_count = cfg.target->seqs().size();
 	db2block_id.reserve(db_count);

src/basic/basic.cpp

@@ -42,7 +42,7 @@ using std::vector;
 using std::count;
 using std::runtime_error;
 
-const char* Const::version_string = "2.1.23";
+const char* Const::version_string = "2.1.24";
 const char* Const::program_name = "diamond";
 
 AlignMode::AlignMode(unsigned mode) :

src/basic/config.cpp

@@ -922,7 +922,7 @@ Config::Config(int argc, const char **argv, bool check_io, CommandLineParser& pa
 	trace_pt_membuf = hit_membuf;
 
 	if (command != Config::version) {
-		static const std::chrono::time_point<std::chrono::system_clock> release_time = std::chrono::system_clock::from_time_t(1771090269);
+		static const std::chrono::time_point<std::chrono::system_clock> release_time = std::chrono::system_clock::from_time_t(1772912406);
 		if (std::chrono::system_clock::now() - release_time > std::chrono::hours(180 * 24)) {
 			set_color(Color::YELLOW, true);
 			cerr << "Warning: This version of DIAMOND is more than 180 days old. It is recommended to always use the latest version." << endl;

src/basic/const.h

@@ -20,7 +20,7 @@ struct Const
 {
 
 	enum {
-		build_version = 177,
+		build_version = 178,
 		max_seed_weight = 32,
 		max_shapes = 64
 	};

src/cluster/cascaded/wrapper.cpp

@@ -45,7 +45,9 @@ using std::bind;
 using std::function;
 using std::runtime_error;
 
-void external();
+namespace External {
+	void external();
+}
 void multinode();
 
 namespace Cluster {
@@ -165,7 +167,8 @@ void Cascaded::run() {
 	init_thresholds();
 	if (!config.parallel_tmpdir.empty()) {
 		if (config.command == ::Config::LINCLUST)
-			multinode();
+			External::external();
+			//multinode();
 		else
 			throw runtime_error("Option is not permitted for this workflow: --parallel-tmpdir");
 		return;

src/cluster/external/align.cpp

@@ -44,6 +44,8 @@ using std::pair;
 using std::ofstream;
 using std::array;
 
+namespace External {
+
 static void align_rep(ThreadPool& tp, const ChunkSeqs& chunk_seqs, vector<PairEntryShort>::const_iterator begin, vector<PairEntryShort>::const_iterator end, int64_t max_oid, BufferArray& out, ofstream* aln_out, ClusterStats &cstats) {
 	const int64_t rep_oid = begin->rep_oid, shift = bit_length(max_oid) - RADIX_BITS;
 	const Sequence rep = chunk_seqs[rep_oid];
@@ -208,4 +210,6 @@ RadixedTable align(Job& job, int chunk_count, int64_t db_size) {
 		if (rep[i] == i)
 			++n;
 	log_stream << n << endl;*/
+}
+
 }

src/cluster/external/build_pair_table.h

@@ -21,6 +21,8 @@ limitations under the License.
 #include "external.h"
 #include "input_buffer.h"
 
+namespace External {
+
 #pragma pack(1)
 
 struct SeedEntry {
@@ -98,4 +100,6 @@ inline void get_pairs_mutual_cov(KeyMergeIterator<InputBuffer<SeedEntry>::ConstI
 				break;
 		}
 	}
+}
+
 }

src/cluster/external/chunk.h

@@ -19,6 +19,8 @@ limitations under the License.
 #include "data/sequence_file.h"
 #include "external.h"
 
+namespace External {
+
 struct ChunkSeqs {
 
 	ChunkSeqs(const std::string& chunk_path) :
@@ -127,4 +129,6 @@ struct ChunkSeqs {
 	std::vector<std::pair<int64_t, int64_t>> oid_range_;
 	std::vector<std::unordered_map<int64_t, Sequence>*> oid2seq_;
 
-};
+};
+
+}