CMakeLists.txt

@@ -47,7 +47,10 @@ endif()
 find_package(ZLIB REQUIRED)
 find_package(Threads REQUIRED)
 
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   set(CMAKE_BUILD_TYPE Release)
+endif()
+
 if(WIN32)
   add_definitions(-D_CRT_SECURE_NO_WARNINGS)
 else()
@@ -60,7 +63,6 @@ include_directories(
 
 add_executable(diamond src/run/main.cpp
   src/basic/config.cpp
-  src/util/tinythread.cpp
   src/basic/score_matrix.cpp
   src/blast/blast_filter.cpp
   src/blast/blast_seg.cpp
@@ -95,15 +97,12 @@ add_executable(diamond src/run/main.cpp
   src/dp/padded_banded_sw.cpp
   src/dp/needleman_wunsch.cpp
   src/output/blast_pairwise_format.cpp
-  src/extra/roc.cpp
   src/dp/comp_based_stats.cpp
-  src/extra/model_sim.cpp
   src/run/double_indexed.cpp
   src/search/collision.cpp
   src/output/sam_format.cpp
   src/align/align.cpp
   src/search/setup.cpp
-  src/extra/opt.cpp
   src/dp/diag_scores.cpp
   src/data/taxonomy.cpp
   src/lib/tantan/tantan.cc
@@ -146,6 +145,10 @@ add_executable(diamond src/run/main.cpp
   src/util/algo/greedy_vortex_cover.cpp
   src/util/algo/greedy_vortex_cover_weighted.cpp
   src/util/sequence/sequence.cpp
+  src/tools/tsv_record.cpp
+  src/tools/tools.cpp
+  src/util/system/getRSS.cpp
+  src/util/math/sparse_matrix.cpp
 )
 
 if(EXTRA)
@@ -154,6 +157,9 @@ if(EXTRA)
       src/extra/benchmark.cpp
 	  src/extra/test.cpp
 	  src/dp/sw_3frame.cpp
+	  src/extra/roc.cpp
+	  src/extra/model_sim.cpp
+	  src/extra/opt.cpp
   )
   add_definitions(-DEXTRA)
 endif()

README.md

@@ -21,6 +21,11 @@ Keep posted about new developments by following me on
 ![image](https://anaconda.org/bioconda/diamond/badges/platforms.svg)
 [![image](https://anaconda.org/bioconda/diamond/badges/downloads.svg)](https://anaconda.org/bioconda/diamond)
 
+Support
+=======
+
+The preferred support channel is the [Diamond community website](http://www.diamondsearch.org/). It provides a platform for users to exchange their experiences and get support directly from the developer. You may also use the GitHub issue tracker or send inquiries by email.
+
 Quick start guide
 =================
 
@@ -32,7 +37,7 @@ quick example for setting up and using the program on Linux.
 Installing the software on your system may be done by downloading it in
 binary format for immediate use:
 
-    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.25/diamond-linux64.tar.gz
     tar xzf diamond-linux64.tar.gz
 
 The extracted `diamond` binary file should be moved to a directory

build_simple.sh

 gcc -c -O3 -DNDEBUG src/blast/sm_blosum45.c src/blast/sm_blosum50.c src/blast/sm_blosum62.c src/blast/sm_blosum80.c src/blast/sm_blosum90.c src/blast/sm_pam30.c src/blast/sm_pam70.c src/blast/sm_pam250.c
-g++ -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \
+g++ -std=gnu++11 -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \
   sm*.o \
   src/run/main.cpp \
   src/basic/config.cpp \
-  src/util/tinythread.cpp \
   src/basic/score_matrix.cpp \
   src/blast/blast_filter.cpp \
   src/blast/blast_seg.cpp \
@@ -30,15 +29,12 @@ g++ -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \
   src/dp/padded_banded_sw.cpp \
   src/dp/needleman_wunsch.cpp \
   src/output/blast_pairwise_format.cpp \
-  src/extra/roc.cpp \
   src/dp/comp_based_stats.cpp \
-  src/extra/model_sim.cpp \
   src/run/double_indexed.cpp \
   src/search/collision.cpp \
   src/output/sam_format.cpp \
   src/align/align.cpp \
   src/search/setup.cpp \
-  src/extra/opt.cpp \
   src/dp/diag_scores.cpp \
   src/data/taxonomy.cpp \
   src/lib/tantan/tantan.cc \
@@ -81,4 +77,8 @@ g++ -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \
   src/util/algo/greedy_vortex_cover.cpp \
   src/util/algo/greedy_vortex_cover_weighted.cpp \
   src/util/sequence/sequence.cpp \
+  src/tools/tsv_record.cpp \
+  src/tools/tools.cpp \
+  src/util/system/getRSS.cpp \
+  src/util/math/sparse_matrix.cpp \
 -lz -lpthread -o diamond

debian/changelog

+diamond-aligner (0.9.25+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Wed, 31 Jul 2019 14:57:15 +0200
+
 diamond-aligner (0.9.24+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-11

debian/control

@@ -3,10 +3,10 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                cmake,
                zlib1g-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/diamond-aligner
 Vcs-Git: https://salsa.debian.org/med-team/diamond-aligner.git
 Homepage: https://github.com/bbuchfink/diamond

src/ChangeLog

+[0.9.25]
+- Added support for the `sscinames` output field to print subject scientific names to the tabular output format.
+- Fixed a compiler error for GCC 8.2.
+- Added option `--stop-match-score` to set the match score of stop codons.
+- Fixed a bug that caused the `qqual` output field to not be correctly clipped to the aligned part of the query.
+- Added output fields `qseq_gapped` and `sseq_gapped` to the tabular format.
+- Raised compiler requirement to GCC 4.8.
+- Fixed a bug that caused the final sequence positions to not be printed in the pairwise format.
+- Allow using `--min-score` instead of `--top` for the LCA computation of the taxonomy output format.
+- Reduced the number of temporary files.
+- Added output field `qstrand` to the tabular format.
+- Database format version changed to 3.
+- Fixed a bug in the `--range-culling` mode that could cause undefined behaviour.
+
 [0.9.24]
 - Fixed a compiler error on macOS.
 - Added --header option to output header for tabular output format.

src/align/align.cpp

@@ -137,14 +137,15 @@ void align_queries(Trace_pt_buffer &trace_pts, Consumer* output_file, const Para
 		timer.go("Computing alignments");
 		Align_fetcher::init(query_range.first, query_range.second, v->begin(), v->end());
 		OutputSink::instance = unique_ptr<OutputSink>(new OutputSink(query_range.first, output_file));
-		Thread_pool threads;
+		vector<thread> threads;
 		if (config.verbosity >= 3 && config.load_balancing == Config::query_parallel)
-			threads.push_back(launch_thread(heartbeat_worker, query_range.second));
+			threads.emplace_back(heartbeat_worker, query_range.second);
 		size_t n_threads = config.load_balancing == Config::query_parallel ? (config.threads_align == 0 ? config.threads_ : config.threads_align) : 1;
 		for (size_t i = 0; i < n_threads; ++i)
 			//threads.push_back(launch_thread(static_cast<void(*)(size_t)>(&align_worker), i));
-			threads.push_back(launch_thread(align_worker, i, &params, &metadata));
-		threads.join_all();
+			threads.emplace_back(align_worker, i, &params, &metadata);
+		for (auto &t : threads)
+			t.join();
 		timer.finish();
 
 		double t = timer.get();

src/align/banded_swipe_pipeline.cpp

@@ -40,9 +40,9 @@ struct Target : public ::Target
 
 	interval ungapped_query_range(int query_dna_len) const
 	{
-		const int i0 = std::max((int)top_hit.query_pos_ - (int)top_hit.subject_pos_, 0),
-			i1 = std::min((int)top_hit.query_pos_ + (int)subject.length() - (int)top_hit.subject_pos_, query_dna_len / 3);
 		const Frame f = Frame(top_hit.frame_);
+		const int i0 = std::max((int)top_hit.query_pos_ - (int)top_hit.subject_pos_, 0),
+			i1 = std::min((int)top_hit.query_pos_ + (int)subject.length() - (int)top_hit.subject_pos_, f.length(query_dna_len));
 		return TranslatedPosition::absolute_interval(TranslatedPosition(i0, f), TranslatedPosition(i1, f), query_dna_len);
 	}
 
@@ -198,11 +198,12 @@ void Pipeline::run(Statistics &stat)
 			const size_t interval_count = (source_query_len + ::Target::INTERVAL - 1) / ::Target::INTERVAL;
 			for (vector<unsigned> &v : intervals)
 				v.resize(interval_count);
-			Thread_pool threads;
+			vector<thread> threads;
 			Atomic<size_t> next(0);
 			for (unsigned i = 0; i < config.threads_; ++i)
-				threads.push_back(launch_thread(build_ranking_worker, targets.begin(), targets.end(), &next, &intervals[i]));
-			threads.join_all();
+				threads.emplace_back(build_ranking_worker, targets.begin(), targets.end(), &next, &intervals[i]);
+			for (auto &t : threads)
+				t.join();
 
 			timer.go("Merging score ranking intervals");
 			for (auto it = intervals.begin() + 1; it < intervals.end(); ++it) {

src/align/query_mapper.h

@@ -22,7 +22,6 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <queue>
 #include <vector>
 #include <list>
-#include "../util/tinythread.h"
 #include "../search/trace_pt_buffer.h"
 #include "../data/queries.h"
 #include "../util/ptr_vector.h"

src/basic/basic.cpp

@@ -24,7 +24,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "sequence.h"
 #include "masking.h"
 
-const char* Const::version_string = "0.9.24";
+const char* Const::version_string = "0.9.25";
 const char* Const::program_name = "diamond";
 const char* Const::id_delimiters = " \a\b\f\n\r\t\v\1";
 

src/basic/config.cpp

@@ -21,7 +21,6 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "config.h"
 #include "../util/util.h"
 #include "../util/log_stream.h"
-#include "../util/tinythread.h"
 #include "../basic/value.h"
 #include "score_matrix.h"
 #include "../util/system.h"
@@ -71,7 +70,9 @@ Config::Config(int argc, const char **argv)
 		.add_command("smith-waterman", "")
 		.add_command("protein-snps", "")
 		.add_command("cluster", "")
-		.add_command("translate", "");
+		.add_command("translate", "")
+		.add_command("filter-blasttab", "")
+		.add_command("show-cbs", "");
 
 	Options_group general("General options");
 	general.add()
@@ -116,7 +117,9 @@ Config::Config(int argc, const char **argv)
 \tsalltitles means All Subject Title(s), separated by a '<>'\n\
 \tqcovhsp means Query Coverage Per HSP\n\
 \tqtitle means Query title\n\
-\tqqual means Query quality values\n\
+\tqqual means Query quality values for the aligned part of the query\n\
+\tfull_qqual means Query quality values\n\
+\tqstrand means Query strand\n\
 \n\tDefault: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore", output_format)
 ("verbose", 'v', "verbose console output", verbose)
 ("log", 0, "enable debug log", debug_log)
@@ -167,6 +170,7 @@ Config::Config(int argc, const char **argv)
 		("no-self-hits", 0, "suppress reporting of identical self hits", no_self_hits)
 		("taxonmap", 0, "protein accession to taxid mapping file", prot_accession2taxid)
 		("taxonnodes", 0, "taxonomy nodes.dmp from NCBI", nodesdmp)
+		("taxonnames", 0, "taxonomy names.dmp from NCBI", namesdmp)
 		("taxonlist", 0, "restrict search to list of taxon ids (comma-separated)", taxonlist);
 
 	Options_group advanced("Advanced options");
@@ -192,7 +196,8 @@ Config::Config(int argc, const char **argv)
 		("range-cover", 0, "percentage of query range to be covered for hit culling (default=50)", query_range_cover, 50.0)
 		("dbsize", 0, "effective database size (in letters)", db_size)
 		("no-auto-append", 0, "disable auto appending of DAA and DMND file extensions", no_auto_append)
-		("xml-blord-format", 0, "Use gnl|BL_ORD_ID| style format in XML output", xml_blord_format);
+		("xml-blord-format", 0, "Use gnl|BL_ORD_ID| style format in XML output", xml_blord_format)
+		("stop-match-score", 0, "Set the match score of stop codons against each other.", stop_match_score, 1);
 
 	Options_group view_options("View options");
 	view_options.add()
@@ -266,7 +271,13 @@ Config::Config(int argc, const char **argv)
 		("use-dataset-field", 0, "", use_dataset_field)
 		("store-query-quality", 0, "", store_query_quality)
 		("swipe-chunk-size", 0, "", swipe_chunk_size, 256u)
-		("query-parallel-limit", 0, "", query_parallel_limit, 1000000u);
+		("query-parallel-limit", 0, "", query_parallel_limit, 1000000u)
+		("hard-masked", 0, "", hardmasked)
+		("cbs-window", 0, "", cbs_window, 40)
+		("tantan-r", 0, "", tantan_r, 0.005)
+		("tantan-s", 0, "", tantan_s, 0.5)
+		("no-unlink", 0, "", no_unlink)
+		("no-dict", 0, "", no_dict);
 		
 	parser.add(general).add(makedb).add(aligner).add(advanced).add(view_options).add(getseq_options).add(hidden_options);
 	parser.store(argc, argv, command);
@@ -361,13 +372,15 @@ Config::Config(int argc, const char **argv)
 			auto_append_extension(output_file, ".gz");
 	}
 
-	message_stream << Const::program_name << " v" << Const::version_string << "." << (unsigned)Const::build_version << " | by Benjamin Buchfink <buchfink@gmail.com>" << endl;
-	message_stream << "Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>" << endl;
-	message_stream << "Check http://github.com/bbuchfink/diamond for updates." << endl << endl;
+	ostream &header_out = command == Config::help ? cout : cerr;
+	header_out << Const::program_name << " v" << Const::version_string << "." << (unsigned)Const::build_version << " | by Benjamin Buchfink <buchfink@gmail.com>" << endl;
+	header_out << "Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>" << endl;
+	header_out << "Check http://github.com/bbuchfink/diamond for updates." << endl << endl;
+	log_stream << Const::program_name << " v" << Const::version_string << "." << (unsigned)Const::build_version << endl;
 #ifndef NDEBUG
 	verbose_stream << "Assertions enabled." << endl;
 #endif
-	set_option(threads_, tthread::thread::hardware_concurrency());
+	set_option(threads_, std::thread::hardware_concurrency());
 
 	switch (command) {
 	case Config::makedb:
@@ -394,7 +407,7 @@ Config::Config(int argc, const char **argv)
 		if (query_range_culling && frame_shift == 0)
 			throw std::runtime_error("Query range culling is only supported in frameshift alignment mode (option -F).");
 		if (matrix_file == "")
-			score_matrix = Score_matrix(to_upper_case(matrix), gap_open, gap_extend, frame_shift);
+			score_matrix = Score_matrix(to_upper_case(matrix), gap_open, gap_extend, frame_shift, stop_match_score);
 		else {
 			if (lambda == 0 || K == 0)
 				throw std::runtime_error("Custom scoring matrices require setting the --lambda and --K options.");

src/basic/config.h

@@ -171,11 +171,19 @@ struct Config
 	bool output_header;
 	string alfmt;
 	string unfmt;
+	string namesdmp;
+	bool hardmasked;
+	int cbs_window;
+	double tantan_r;
+	double tantan_s;
+	bool no_unlink;
+	bool no_dict;
+	int stop_match_score;
 
 	enum {
 		makedb = 0, blastp = 1, blastx = 2, view = 3, help = 4, version = 5, getseq = 6, benchmark = 7, random_seqs = 8, compare = 9, sort = 10, roc = 11, db_stat = 12, model_sim = 13,
 		match_file_stat = 14, model_seqs = 15, opt = 16, mask = 17, fastq2fasta = 18, dbinfo = 19, test_extra = 20, test_io = 21, db_annot_stats = 22, read_sim = 23, info = 24, seed_stat = 25,
-		smith_waterman = 26, protein_snps = 27, cluster = 28, translate = 29
+		smith_waterman = 26, protein_snps = 27, cluster = 28, translate = 29, filter_blasttab = 30, show_cbs = 31
 	};
 	unsigned	command;
 

src/basic/const.h

@@ -23,7 +23,7 @@ struct Const
 {
 
 	enum {
-		build_version = 125,
+		build_version = 126,
 		seedp_bits = 10,
 		seedp = 1<<seedp_bits,
 		max_seed_weight = 32,

src/basic/masking.cpp

@@ -46,20 +46,20 @@ void Masking::operator()(Letter *seq, size_t len) const
 {
 	tantan::maskSequences((tantan::uchar*)seq, (tantan::uchar*)(seq + len), 50,
 		(tantan::const_double_ptr*)probMatrixPointers_,
-		0.005, 0.05,
+		config.tantan_r, 0.05,
 		0.9,
 		0, 0,
-		0.5, (const tantan::uchar*)mask_table_x_);
+		config.tantan_s, (const tantan::uchar*)mask_table_x_);
 }
 
 void Masking::mask_bit(Letter *seq, size_t len) const
 {
 	tantan::maskSequences((tantan::uchar*)seq, (tantan::uchar*)(seq + len), 50,
 		(tantan::const_double_ptr*)probMatrixPointers_,
-		0.005, 0.05,
+		config.tantan_r, 0.05,
 		0.9,
 		0, 0,
-		0.5, (const tantan::uchar*)mask_table_bit_);
+		config.tantan_s, (const tantan::uchar*)mask_table_bit_);
 }
 
 void Masking::bit_to_hard_mask(Letter *seq, size_t len, size_t &n) const
@@ -90,9 +90,10 @@ void mask_worker(Atomic<size_t> *next, Sequence_set *seqs, const Masking *maskin
 
 void mask_seqs(Sequence_set &seqs, const Masking &masking, bool hard_mask)
 {
-	Thread_pool threads;
+	vector<thread> threads;
 	Atomic<size_t> next(0);
 	for (size_t i = 0; i < config.threads_; ++i)
-		threads.push_back(launch_thread(mask_worker, &next, &seqs, &masking, hard_mask));
-	threads.join_all();
+		threads.emplace_back(mask_worker, &next, &seqs, &masking, hard_mask);
+	for (auto &t : threads)
+		t.join();
 }
\ No newline at end of file

src/basic/score_matrix.cpp

@@ -212,18 +212,18 @@ const Matrix_info Matrix_info::matrices[] = {
 	{ "DNA", dna_values, (const char*)DNA_scores, 1, 4, 2 }
 };
 
-Score_matrix::Score_matrix(const string & matrix, int gap_open, int gap_extend, int frameshift, uint64_t db_letters):
+Score_matrix::Score_matrix(const string & matrix, int gap_open, int gap_extend, int frameshift, int stop_match_score, uint64_t db_letters):
 	gap_open_ (gap_open == -1 ? Matrix_info::get(matrix).default_gap_open : gap_open),
 	gap_extend_ (gap_extend == -1 ? Matrix_info::get(matrix).default_gap_extend : gap_extend),
 	frame_shift_(frameshift),
 	db_letters_ ((double)db_letters),
 	constants_ (Matrix_info::get(matrix).get_constants(gap_open_, gap_extend_)),
 	name_(matrix),
-	matrix8_(Matrix_info::get(matrix).scores),
+	matrix8_(Matrix_info::get(matrix).scores, stop_match_score),
 	bias_((char)(-low_score())),
-	matrix8u_(Matrix_info::get(matrix).scores, bias_),
-	matrix16_(Matrix_info::get(matrix).scores),
-	matrix32_(Matrix_info::get(matrix).scores)
+	matrix8u_(Matrix_info::get(matrix).scores, stop_match_score, bias_),
+	matrix16_(Matrix_info::get(matrix).scores, stop_match_score),
+	matrix32_(Matrix_info::get(matrix).scores, stop_match_score)
 { }
 
 char Score_matrix::low_score() const

src/basic/score_matrix.h

@@ -36,7 +36,7 @@ struct Score_matrix
 {
 
 	Score_matrix() {}
-	Score_matrix(const string &matrix, int gap_open, int gap_extend, int frame_shift, uint64_t db_letters = 0);
+	Score_matrix(const string &matrix, int gap_open, int gap_extend, int frame_shift, int stop_match_score, uint64_t db_letters = 0);
 	Score_matrix(const string &matrix_file, double lambda, double K, int gap_open, int gap_extend, uint64_t db_letters = 0);
 
 	friend std::ostream& operator<<(std::ostream& s, const Score_matrix &m);
@@ -137,12 +137,14 @@ private:
 	struct Scores
 	{
 		Scores() {}
-		Scores(const char *scores, char bias = 0)
+		Scores(const char *scores, int stop_match_score = 1, char bias = 0)
 		{
 			const unsigned n = value_traits.alphabet_size;
 			for (unsigned i = 0; i < 32; ++i)
 				for (unsigned j = 0; j < 32; ++j)
 					data[i * 32 + j] = i < n && j < n ? (_t)(scores[i*n + j] + (int)bias) : -(std::numeric_limits<_t>::max() / 2);
+			if (stop_match_score != 1)
+				data[24 * 32 + 24] = stop_match_score;
 		}
 #ifdef _MSC_VER
 		__declspec(align(16)) _t data[32 * 32];

src/basic/sequence.h

@@ -21,6 +21,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <iostream>
 #include <vector>
+#include <string>
 #include "../basic/value.h"
 #include "../util/binary_buffer.h"
 #include "../util/text_buffer.h"
@@ -32,6 +33,7 @@ struct sequence
 {
 	static const char DELIMITER = '\x1f';
 	struct Reversed {};
+	struct Hardmasked {};
 	sequence():
 		len_ (0),
 		clipping_offset_ (0),
@@ -125,6 +127,17 @@ struct sequence
 		}
 		return os;
 	}
+	TextBuffer& print(TextBuffer &os, const Value_traits &v, Hardmasked) const
+	{
+		for (unsigned i = 0; i < len_; ++i) {
+			long l = (long)data_[i];
+			if ((l & 128) == 0)
+				os << v.alphabet[l];
+			else
+				os << v.alphabet[(long)v.mask_char];
+		}
+		return os;
+	}
 	TextBuffer& print(TextBuffer &os, const Value_traits &v, Reversed) const
 	{
 		for (int i = (int)len_ - 1; i >= 0; --i)
@@ -135,6 +148,9 @@ struct sequence
 	{
 		return sequence(*this, begin, end - 1);
 	}
+	std::string substr(int begin, int end) const {
+		return std::string(&data_[begin], &data_[end]);
+	}
 	friend TextBuffer& operator<<(TextBuffer &buf, const sequence &s)
 	{
 		return s.print(buf, value_traits);

src/basic/statistics.h

@@ -22,7 +22,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <algorithm>
 #include <stdint.h>
 #include <string.h>
-#include "../util/tinythread.h"
+#include <mutex>
 #include "../util/log_stream.h"
 #include "../util/memory/memory_pool.h"
 
@@ -101,7 +101,7 @@ struct Statistics
 	}
 
 	stat_type data_[COUNT];
-	tthread::mutex mtx_;
+	std::mutex mtx_;
 
 };
 

src/basic/translated_position.h

@@ -19,6 +19,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #ifndef TRANSLATED_POSITION_H_
 #define TRANSLATED_POSITION_H_
 
+#include <algorithm>
 #include "../util/interval.h"
 
 enum Strand { FORWARD = 0, REVERSE = 1 };
@@ -43,6 +44,10 @@ struct Frame
 	{
 		return (offset + 1) * (strand == FORWARD ? 1 : -1);
 	}
+	int length(int dna_len) const
+	{
+		return std::max((dna_len - offset) / 3, 0);
+	}
 	int offset;
 	Strand strand;
 };