New upstream version 0.9.19+dfsg

project (DIAMOND)

option(BUILD_STATIC "BUILD_STATIC" OFF)

option(EXTRA "EXTRA" OFF)

if(BUILD_STATIC)

    set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")

add_executable(diamond src/run/main.cpp

  src/basic/config.cpp

  src/util/tinythread.cpp

  src/util/compressed_stream.cpp

  src/basic/score_matrix.cpp

  src/blast/blast_filter.cpp

  src/blast/blast_seg.cpp

  src/dp/banded_sw.cpp

  src/data/sorted_list.cpp

  src/data/seed_set.cpp

  src/util/binary_file.cpp

  src/util/simd.cpp

  src/output/taxon_format.cpp

  src/output/view.cpp

  src/dp/swipe/banded_3frame_swipe.cpp

  src/dp/swipe/banded_swipe.cpp

  src/align/banded_swipe_pipeline.cpp

  src/data/ref_dictionary.cpp

  src/util/io/compressed_stream.cpp

  src/util/io/deserializer.cpp

  src/util/io/file_sink.cpp

  src/util/io/file_source.cpp

  src/util/io/input_file.cpp

  src/util/io/input_stream_buffer.cpp

  src/util/io/output_file.cpp

  src/util/io/output_stream_buffer.cpp

  src/util/io/serializer.cpp

  src/util/io/temp_file.cpp

  src/util/io/text_input_file.cpp

  src/data/taxon_list.cpp

  src/data/taxonomy_nodes.cpp

  src/util/algo/MurmurHash3.cpp

)

if(EXTRA)

  target_sources(diamond

    PUBLIC

      src/extra/benchmark.cpp

	  src/extra/test.cpp

	  src/dp/sw_3frame.cpp

  )

  add_definitions(-DEXTRA)

endif()

target_link_libraries(diamond ${ZLIB_LIBRARY} ${CMAKE_THREAD_LIBS_INIT})

install(TARGETS diamond DESTINATION bin)

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Quick start guide

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/v0.9.17/diamond-linux64.tar.gz

    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.19/diamond-linux64.tar.gz

    tar xzf diamond-linux64.tar.gz

The extracted ``diamond`` binary file should be moved to a directory contained in your executable search path (PATH environment variable).

DIAMOND is developed by Benjamin Buchfink. Feel free to contact me for support (`Email <mailto:buchfink@gmail.com>`_ `Twitter <http://twitter.com/bbuchfink>`_).

If you use DIAMOND in published research, please cite B. Buchfink, Xie C., D. Huson, "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12, 59-60 (2015).

.. image:: https://ga-beacon.appspot.com/UA-109667396-1/diamond?pixel

  src/run/main.cpp \

  src/basic/config.cpp \

  src/util/tinythread.cpp \

  src/util/compressed_stream.cpp \

  src/basic/score_matrix.cpp \

  src/blast/blast_filter.cpp \

  src/blast/blast_seg.cpp \

  src/dp/banded_sw.cpp \

  src/data/sorted_list.cpp \

  src/data/seed_set.cpp \

  src/util/binary_file.cpp \

  src/util/simd.cpp \

  src/output/taxon_format.cpp \

  src/output/view.cpp \

  src/dp/swipe/banded_3frame_swipe.cpp \

  src/dp/swipe/banded_swipe.cpp \

  src/align/banded_swipe_pipeline.cpp \

  src/data/ref_dictionary.cpp \

  src/util/io/compressed_stream.cpp \

  src/util/io/deserializer.cpp \

  src/util/io/file_sink.cpp \

  src/util/io/file_source.cpp \

  src/util/io/input_file.cpp \

  src/util/io/input_stream_buffer.cpp \

  src/util/io/output_file.cpp \

  src/util/io/output_stream_buffer.cpp \

  src/util/io/serializer.cpp \

  src/util/io/temp_file.cpp \

  src/util/io/text_input_file.cpp \

  src/data/taxon_list.cpp \

  src/data/taxonomy_nodes.cpp \

  src/util/algo/MurmurHash3.cpp \

-lz -lpthread -o diamond

[0.9.19]

- Fixed a bug in the --un function to write unaligned reads.

- Fixed an issue in the LCA algorithm that could cause an assignment to a higher node.

- --taxonmap and --taxonnodes parameters now apply exclusively to the makedb command.

- Added option --taxonlist to filter searches by subject taxonomic id.

- Changed database format; rebuilding is required.

[0.9.18]

- Optimized output writing performance.

- Fixed a bug in the XML output format.

[0.9.17]

- Fixed a compiler error on FreeBSD.

- Added option --range-culling.

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

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

void align_worker(size_t thread_id)

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

{

	Align_fetcher hits;

	Statistics stat;

				buf = new TextBuffer;

				const char *query_title = query_ids::get()[hits.query].c_str();

				output_format->print_query_intro(hits.query, query_title, get_source_query_len((unsigned)hits.query), *buf, true);

				output_format->print_query_epilog(*buf, query_title, true);

				output_format->print_query_epilog(*buf, query_title, true, *params);

			}

			OutputSink::get().push(hits.query, buf);

			continue;

		QueryMapper *mapper;

		if (config.ext == Config::swipe)

			mapper = new ExtensionPipeline::Swipe::Pipeline(hits.query, hits.begin, hits.end);

			mapper = new ExtensionPipeline::Swipe::Pipeline(*params, hits.query, hits.begin, hits.end);

		else if (config.frame_shift != 0)

			mapper = new ExtensionPipeline::BandedSwipe::Pipeline(hits.query, hits.begin, hits.end, dp_stat);

			mapper = new ExtensionPipeline::BandedSwipe::Pipeline(*params, hits.query, hits.begin, hits.end, dp_stat);

		else

			mapper = new ExtensionPipeline::Greedy::Pipeline(hits.query, hits.begin, hits.end);

			mapper = new ExtensionPipeline::Greedy::Pipeline(*params, hits.query, hits.begin, hits.end);

		mapper->init();

		mapper->run(stat);

		TextBuffer *buf = 0;

		if (*output_format != Output_format::null) {

			buf = new TextBuffer;

			const bool aligned = mapper->generate_output(*buf, stat);

			const bool aligned = mapper->generate_output(*buf, stat, *metadata);

			if (aligned && !config.unaligned.empty())

				query_aligned[hits.query] = true;

		}

	::dp_stat += dp_stat;

}

void align_queries(Trace_pt_buffer &trace_pts, Output_stream* output_file)

void align_queries(Trace_pt_buffer &trace_pts, OutputFile* output_file, const Parameters &params, const Metadata &metadata)

{

	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;

			threads.push_back(launch_thread(heartbeat_worker, query_range.second));

		size_t n_threads = (config.threads_align == 0 ? config.threads_ : config.threads_align);

		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(static_cast<void(*)(size_t)>(&align_worker), i));

			threads.push_back(launch_thread(align_worker, i, &params, &metadata));

		threads.join_all();

		timer.finish();