Added merge-daa workflow.

src/output/daa/daa_file.h

@@ -217,4 +217,6 @@ struct DAA_file
 	PtrVector<string> ref_name_;
 	vector<uint32_t> ref_len_;
 
+	friend void write_file(DAA_file&, OutputFile&);
+
 };

src/output/daa/merge.cpp

@@ -1,5 +1,71 @@
+/****
+DIAMOND protein aligner
+Copyright (C) 2022 Max Planck Society for the Advancement of Science e.V.
+
+Code developed by Benjamin Buchfink <benjamin.buchfink@tue.mpg.de>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+****/
+
+#include <unordered_map>
+#include "../../basic/config.h"
 #include "daa_file.h"
+#include "daa_write.h"
 
-void merge_daa() {
+using std::unordered_map;
+using std::string;
+
+unordered_map<int64_t, int64_t> build_mapping(unordered_map<string, int64_t>& acc2oid, DAA_file& f) {
+	unordered_map<int64_t, int64_t> r;
+	for (int64_t i = 0; i < f.db_seqs_used(); ++i) {
+		auto it = acc2oid.emplace(f.ref_name(i), acc2oid.size());
+		r.emplace(i, it.first->second);
+	}
+	return r;
+}
 
+static void write_file(DAA_file& f, OutputFile& out) {
+	uint32_t size = 0;
+	BinaryBuffer buf;
+	TextBuffer out_buf;
+	size_t query_num;
+	while (f.read_query_buffer(buf, query_num)) {
+		DAA_query_record r(f, buf, query_num);
+		size_t seek_pos = write_daa_query_record(out_buf, r.query_name.c_str(), r.query_seq.source());
+		DAA_query_record::Match_iterator i = r.begin();
+		for (; i.good(); ++i) {
+			write_daa_record(out_buf, *i, i->subject_id);
+		}
+		finish_daa_query_record(out_buf, seek_pos);
+		out.write(out_buf.data(), out_buf.size());
+		out_buf.clear();
+	}
+}
+
+void merge_daa() {
+	vector<DAA_file*> files;
+	const int n = config.input_ref_file.size();
+	unordered_map<string, int64_t> acc2oid;
+	vector<unordered_map<int64_t, int64_t>> oid_maps;
+	oid_maps.reserve(n);
+	for (int i = 0; i < n; ++i) {
+		files.push_back(new DAA_file(config.input_ref_file[i]));
+		oid_maps.push_back(build_mapping(acc2oid, *files.back()));
+	}
+	OutputFile out(config.output_file);
+	init_daa(out);
+	for (DAA_file* f : files)
+		write_file(*f, out);
+	out.close();
 }