New upstream version 0.9.28+dfsg

option(EXTRA "EXTRA" OFF)

option(STATIC_LIBGCC "STATIC_LIBGCC" OFF)

option(STATIC_LIBSTDC++ "STATIC_LIBSTDC++" OFF)

option(SSSE3 "SSSE3" OFF)

option(POPCNT "POPCNT" OFF)

IF(STATIC_LIBSTDC++)

  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libstdc++")

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=gnu++11")

endif()

if(SSSE3)

  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mssse3")

  if(POPCNT)

    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")

  endif()

elseif(CMAKE_BUILD_MARCH)

if(CMAKE_BUILD_MARCH)

  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${CMAKE_BUILD_MARCH}")

else()

  include(CheckCXXCompilerFlag)

  CHECK_CXX_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCHNATIVE)

  if(COMPILER_SUPPORTS_MARCHNATIVE)

    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")

  endif()

endif()

find_package(ZLIB REQUIRED)

endif()

if(WIN32)

  add_definitions(-D_CRT_SECURE_NO_WARNINGS)

  add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_ITERATOR_DEBUG_LEVEL=0)

else()

  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable")

endif()

  "${CMAKE_SOURCE_DIR}/src"

  "${ZLIB_INCLUDE_DIR}")

add_executable(diamond src/run/main.cpp

set(DISPATCH_OBJECTS

"src/dp/swipe/banded_3frame_swipe.cpp"

"src/dp/swipe/swipe.cpp"

"src/dp/swipe/banded_swipe.cpp"

"src/search/collision.cpp"

"src/search/stage1.cpp"

"src/search/stage2.cpp"

"src/tools/benchmark.cpp"

"src/dp/swipe/swipe_wrapper.cpp"

)

add_library(arch_generic OBJECT ${DISPATCH_OBJECTS})

target_compile_options(arch_generic PUBLIC -DDISPATCH_ARCH=ARCH_GENERIC)

add_library(arch_sse4_1 OBJECT ${DISPATCH_OBJECTS})

target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -mssse3 -mpopcnt -msse4.1)

add_executable(diamond $<TARGET_OBJECTS:arch_generic>

  $<TARGET_OBJECTS:arch_sse4_1>

  src/run/main.cpp

  src/basic/config.cpp

  src/basic/score_matrix.cpp

  src/blast/blast_filter.cpp

  src/data/reference.cpp

  src/data/seed_histogram.cpp

  src/output/daa_record.cpp

  src/search/search.cpp

  src/util/command_line_parser.cpp

  src/util/seq_file_format.cpp

  src/util/util.cpp 

  src/dp/ungapped_align.cpp

  src/run/tools.cpp

  src/dp/greedy_align.cpp

  src/search/stage2.cpp

  src/output/output_format.cpp

  src/output/join_blocks.cpp

  src/data/frequent_seeds.cpp

  src/output/blast_pairwise_format.cpp

  src/dp/comp_based_stats.cpp

  src/run/double_indexed.cpp

  src/search/collision.cpp

  src/output/sam_format.cpp

  src/align/align.cpp

  src/search/setup.cpp

  src/data/taxonomy.cpp

  src/lib/tantan/tantan.cc

  src/basic/masking.cpp

  src/dp/swipe/swipe.cpp

  src/dp/banded_sw.cpp

  src/data/sorted_list.cpp

  src/data/seed_set.cpp

  src/util/simd.cpp

  src/output/taxon_format.cpp

  src/output/target_culling.cpp

  src/align/greedy_pipeline.cpp

  src/align/swipe_pipeline.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/data/taxonomy_nodes.cpp

  src/util/algo/MurmurHash3.cpp

  src/search/stage0.cpp

  src/util/memory/memory_pool.cpp

  src/data/seed_array.cpp

  src/output/paf_format.cpp

  src/util/system/system.cpp

  src/util/system/getRSS.cpp

  src/util/math/sparse_matrix.cpp

  src/lib/tantan/LambdaCalculator.cc

  src/data/taxonomy_filter.cpp

)

if(EXTRA)

[![Build Status](https://travis-ci.org/bbuchfink/diamond.svg?branch=master)](https://travis-ci.org/bbuchfink/diamond)

[![image](https://anaconda.org/bioconda/diamond/badges/version.svg)](https://anaconda.org/bioconda/diamond)

![image](https://anaconda.org/bioconda/diamond/badges/platforms.svg)

[![image](https://anaconda.org/bioconda/diamond/badges/downloads.svg)](https://anaconda.org/bioconda/diamond)

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/v0.9.26/diamond-linux64.tar.gz

    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.28/diamond-linux64.tar.gz

    tar xzf diamond-linux64.tar.gz

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

  src/util/system/getRSS.cpp \

  src/util/math/sparse_matrix.cpp \

  src/lib/tantan/LambdaCalculator.cc \

  src/data/taxonomy_filter.cpp \

-lz -lpthread -o diamond

[0.9.28]

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

- Fixed a clang compiler error.

[0.9.27]

- Improved performance of the seed matching stage.

- Seed frequency counts are computed based on hit seeds.

- Added option `--taxon-exclude` to exclude list of taxon ids from search.

- Compiling from source will no longer perform a native build. Instead, a portable binary that contains code paths

  for multiple architectures will be produced, with dispatch logic that is invoked at runtime.

[0.9.26]

- Fixed a bug that could cause undefined behaviour when using a database file of format version < 2.

- Fixed a compiler error when compiled as generic C++.

		QueryMapper *mapper;

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

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

		else if (config.frame_shift != 0)

		else if (config.frame_shift != 0 || config.ext == Config::banded_swipe)

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

		else

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

			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.emplace_back(align_worker, i, &params, &metadata);

		for (auto &t : threads)

			t.join();