Commit 0238729e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.9.24+dfsg

parent e06c99fd

CMakeLists.txt

+24 −1
Original line number Diff line number Diff line
@@ -3,6 +3,18 @@ project (DIAMOND) 


option(BUILD_STATIC "BUILD_STATIC" OFF)

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++")

endif()



IF(STATIC_LIBGCC)

  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libgcc")

endif()



if(BUILD_STATIC)

    set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
@@ -12,7 +24,17 @@ endif() 


set(CMAKE_CXX_STANDARD 11)



if(CMAKE_BUILD_MARCH)

if (${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)

else()

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)

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

else()

  include(CheckCXXCompilerFlag)
@@ -123,6 +145,7 @@ add_executable(diamond src/run/main.cpp 
  src/run/cluster.cpp

  src/util/algo/greedy_vortex_cover.cpp

  src/util/algo/greedy_vortex_cover_weighted.cpp

  src/util/sequence/sequence.cpp

)



if(EXTRA)

README.md

+1 −1
Original line number Diff line number Diff line
@@ -32,7 +32,7 @@ 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/v0.9.23/diamond-linux64.tar.gz

    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz

    tar xzf diamond-linux64.tar.gz



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

build_simple.sh

+1 −0
Original line number Diff line number Diff line
@@ -80,4 +80,5 @@ g++ -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \ 
  src/run/cluster.cpp \

  src/util/algo/greedy_vortex_cover.cpp \

  src/util/algo/greedy_vortex_cover_weighted.cpp \

  src/util/sequence/sequence.cpp \

-lz -lpthread -o diamond

src/ChangeLog

+13 −0
Original line number Diff line number Diff line 
[0.9.24]

- Fixed a compiler error on macOS.

- Added --header option to output header for tabular output format.

- The quality string output in tabular format (qqual field) is clipped to the aligned part of the query.

- Print '*' as quality string if quality values are not available in tabular output format.

- Added field 'full_qqual' to print unclipped query quality values to the tabular format.

- Added field 'full_qseq' to print unclipped query sequence to the tabular format.

- Added support for using the hyphen character '-' to denote the standard input for input file parameters.

- Status messages are written to stderr.

- Fixed a bug that could incorrectly report queries as unaligned in the output of the --un option.

- Added option '--al' to write aligned queries to file.

- Added options '--alfmt' and '--unfmt' to set the format of the aligned/unaligned query file (supported values: fasta, fastq).



[0.9.23]

- Fixed an issue that could cause too high memory usage.

- Added output field 'qqual' to print query FASTQ quality values to the tabular format.

src/align/align.cpp

+4 −1
Original line number Diff line number Diff line
@@ -105,8 +105,11 @@ void align_worker(size_t thread_id, const Parameters *params, const Metadata *me 
		if (*output_format != Output_format::null) {

			buf = new TextBuffer;

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

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

			if (aligned && (!config.unaligned.empty() || !config.aligned_file.empty())) {

				query_aligned_mtx.lock();

				query_aligned[hits.query] = true;

				query_aligned_mtx.unlock();

			}

		}

		delete mapper;

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