Commit 2809b67e authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 0.9.29+dfsg

parent 8da09bec

README.md

+1 −1
Original line number Diff line number Diff line
@@ -31,7 +31,7 @@ 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/v0.9.28/diamond-linux64.tar.gz

    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.29/diamond-linux64.tar.gz

    tar xzf diamond-linux64.tar.gz



The extracted `diamond` binary file should be moved to a directory

src/ChangeLog

+3 −0
Original line number Diff line number Diff line 
[0.9.29]

- Fixed a bug that could cause taxonomy features to function incorrectly for databases created by versions 0.9.27 and 0.9.28.



[0.9.28]

- Fixed a bug that could cause alignment score overflows for scores > 65535 in frameshift alignment mode.

- Fixed a clang compiler error.

src/align/align.cpp

+11 −4
Original line number Diff line number Diff line
@@ -70,13 +70,13 @@ unique_ptr<Queue> Align_fetcher::queue_; 
vector<hit>::iterator Align_fetcher::it_;

vector<hit>::iterator Align_fetcher::end_;



void align_worker(size_t thread_id, const Parameters *params, const Metadata *metadata)

void align_worker(size_t thread_id, const Parameters *params, const Metadata *metadata, const sequence *subjects, size_t subject_count)

{

	Align_fetcher hits;

	Statistics stat;

	DpStat dp_stat;

	while (hits.get()) {

		if (hits.end == hits.begin) {

		if ((hits.end == hits.begin) && subjects == nullptr) {

			TextBuffer *buf = 0;

			if (!blocked_processing && *output_format != Output_format::daa && config.report_unaligned != 0) {

				buf = new TextBuffer;
@@ -98,7 +98,7 @@ void align_worker(size_t thread_id, const Parameters *params, const Metadata *me 
		task_timer timer("Initializing mapper", hits.target_parallel ? 3 : UINT_MAX);

		mapper->init();

		timer.finish();

		mapper->run(stat);

		mapper->run(stat, subjects, subject_count);



		timer.go("Generating output");

		TextBuffer *buf = 0;
@@ -123,6 +123,13 @@ void align_queries(Trace_pt_buffer &trace_pts, Consumer* output_file, const Para 
{

	const size_t max_size = (size_t)std::min(config.chunk_size*1e9 * 9 * 2 / config.lowmem, 2e9);

	pair<size_t, size_t> query_range;

	vector<sequence> subjects;

	if (config.swipe_all) {

		subjects.reserve(ref_seqs::get().get_length());

		for (size_t i = 0; i < ref_seqs::get().get_length(); ++i)

			subjects.push_back(ref_seqs::get()[i]);

	}



	while (true) {

		task_timer timer("Loading trace points", 3);

		Trace_pt_list *v = new Trace_pt_list;
@@ -142,7 +149,7 @@ void align_queries(Trace_pt_buffer &trace_pts, Consumer* output_file, const Para 
			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.emplace_back(align_worker, i, &params, &metadata);

			threads.emplace_back(align_worker, i, &params, &metadata, subjects.empty() ? nullptr : subjects.data(), subjects.size());

		for (auto &t : threads)

			t.join();

		timer.finish();

src/align/align.h

+3 −3
Original line number Diff line number Diff line
@@ -75,7 +75,7 @@ namespace ExtensionPipeline { 
				QueryMapper(params, query_id, begin, end)

			{}

			Target& target(size_t i);

			virtual void run(Statistics &stat);

			virtual void run(Statistics &stat, const sequence *subjects = nullptr, size_t subject_count = 0);

			virtual ~Pipeline() {}

		};

	}
@@ -85,7 +85,7 @@ namespace ExtensionPipeline { 
			Pipeline(const Parameters &params, size_t query_id, Trace_pt_list::iterator begin, Trace_pt_list::iterator end) :

				QueryMapper(params, query_id, begin, end)

			{}

			virtual void run(Statistics &stat);

			virtual void run(Statistics &stat, const sequence *subjects = nullptr, size_t subject_count = 0);

			virtual ~Pipeline() {}

		};

	}
@@ -98,7 +98,7 @@ namespace ExtensionPipeline { 
				dp_stat(dp_stat)

			{}

			Target& target(size_t i);

			virtual void run(Statistics &stat);

			virtual void run(Statistics &stat, const sequence *subjects = nullptr, size_t subject_count = 0);

			void run_swipe(bool score_only);

			void range_ranking();

			DpStat &dp_stat;

src/align/banded_swipe_pipeline.cpp

+9 −7
Original line number Diff line number Diff line
@@ -154,18 +154,20 @@ void Pipeline::run_swipe(bool score_only) 
	vector<DpTarget> vf, vr;

	for (size_t i = 0; i < n_targets(); ++i)

		target(i).add(*this, vf, vr, (int)i);

	list<Hsp> hsp;

	if (score_matrix.frame_shift()) {

		list<Hsp> hsp = banded_3frame_swipe(translated_query, FORWARD, vf.begin(), vf.end(), this->dp_stat, score_only, target_parallel);

		hsp = banded_3frame_swipe(translated_query, FORWARD, vf.begin(), vf.end(), this->dp_stat, score_only, target_parallel);

		hsp.splice(hsp.end(), banded_3frame_swipe(translated_query, REVERSE, vr.begin(), vr.end(), this->dp_stat, score_only, target_parallel));

	}

	else {

		hsp = DP::BandedSwipe::swipe(query_seq(0), vf.begin(), vf.end(), Frame(0), query_cb[0], score_only ? 0 : DP::TRACEBACK);

	}

	

	while (!hsp.empty()) {

		list<Hsp> &l = target(hsp.begin()->swipe_target).hsps;

		l.splice(l.end(), hsp, hsp.begin());

	}

}

	else {

		DP::BandedSwipe::swipe(query_seq(0), vf.begin(), vf.end(), Frame(0), score_only ? 0 : DP::TRACEBACK);

	}

}



void build_ranking_worker(PtrVector<::Target>::iterator begin, PtrVector<::Target>::iterator end, Atomic<size_t> *next, vector<unsigned> *intervals) {

	PtrVector<::Target>::iterator it;
@@ -177,7 +179,7 @@ void build_ranking_worker(PtrVector<::Target>::iterator begin, PtrVector<::Targe 
	}

}



void Pipeline::run(Statistics &stat)

void Pipeline::run(Statistics &stat, const sequence *subjects, size_t subject_count)

{

	task_timer timer("Init banded swipe pipeline", target_parallel ? 3 : UINT_MAX);

	Config::set_option(config.padding, 32);