Commit 0bdf5d93 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.9.22+dfsg

parent 919afe99

CMakeLists.txt

+1 −0
Original line number Diff line number Diff line
@@ -112,6 +112,7 @@ add_executable(diamond src/run/main.cpp 
  src/search/stage0.cpp

  src/util/memory/memory_pool.cpp

  src/data/seed_array.cpp

  src/output/paf_format.cpp

)



if(EXTRA)

README.rst

+2 −2
Original line number Diff line number Diff line
@@ -16,7 +16,7 @@ Keep posted about new developments by following me on Twitter. 
   :target: https://gitter.im/diamond-aligner/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge

.. image:: https://anaconda.org/bioconda/diamond/badges/downloads.svg

   :target: https://anaconda.org/bioconda/diamond

.. image:: https://img.shields.io/badge/Google%20Scholar-523-blue.svg

.. image:: https://img.shields.io/badge/Google%20Scholar-546-blue.svg

   :target: https://scholar.google.de/citations?user=kjPIF1cAAAAJ



Quick start guide
@@ -25,7 +25,7 @@ Please read the `manual <https://github.com/bbuchfink/diamond/raw/master/diamond 


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/v0.9.21/diamond-linux64.tar.gz

    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.22/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).

build_simple.sh

+1 −0
Original line number Diff line number Diff line
@@ -75,4 +75,5 @@ g++ -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \ 
  src/search/stage0.cpp \

  src/util/memory/memory_pool.cpp \

  src/data/seed_array.cpp \

  src/output/paf_format.cpp \

-lz -lpthread -o diamond

src/ChangeLog

+6 −0
Original line number Diff line number Diff line 
[0.9.22]

- Added output field full_sseq to tabular output format.

- Database sequences that exceed the maximum accession length will no longer cause an error.

- Added support for PAF output format.

- Optimized performance of database taxonomy filtering.



[0.9.21]

- Fixed compiler errors on some systems.

src/align/query_mapper.cpp

+9 −7
Original line number Diff line number Diff line
@@ -195,8 +195,9 @@ bool QueryMapper::generate_output(TextBuffer &buffer, Statistics &stat, const Me 
			|| score_matrix.bitscore(targets[i].filter_score) < config.min_bit_score)

			break;



		const unsigned subject_len = (unsigned)ref_seqs::get()[targets[i].subject_id].length();

		const char *ref_title = ref_ids::get()[targets[i].subject_id].c_str();

		const size_t subject_id = targets[i].subject_id;

		const unsigned subject_len = (unsigned)ref_seqs::get()[subject_id].length();

		const char *ref_title = ref_ids::get()[subject_id].c_str();

		targets[i].apply_filters(source_query_len, subject_len, query_title, ref_title);

		if (targets[i].hsps.size() == 0)

			continue;
@@ -219,7 +220,7 @@ bool QueryMapper::generate_output(TextBuffer &buffer, Statistics &stat, const Me 
			if (blocked_processing) {

				if (n_hsp == 0)

					seek_pos = IntermediateRecord::write_query_intro(buffer, query_id);

				IntermediateRecord::write(buffer, *j, query_id, targets[i].subject_id);

				IntermediateRecord::write(buffer, *j, query_id, subject_id);

			}

			else {

				if (n_hsp == 0) {
@@ -229,18 +230,19 @@ bool QueryMapper::generate_output(TextBuffer &buffer, Statistics &stat, const Me 
						f->print_query_intro(query_id, query_title, source_query_len, buffer, false);

				}

				if (*f == Output_format::daa)

					write_daa_record(buffer, *j, query_id, targets[i].subject_id);

					write_daa_record(buffer, *j, query_id, subject_id);

				else

					f->print_match(Hsp_context(*j,

						query_id,

						translated_query,

						query_title,

						targets[i].subject_id,

						ReferenceDictionary::get().block_to_database_id(targets[i].subject_id),

						subject_id,

						ReferenceDictionary::get().block_to_database_id(subject_id),

						ref_title,

						subject_len,

						n_target_seq,

						hit_hsps), metadata, buffer);

						hit_hsps,

						ref_seqs::get()[subject_id]), metadata, buffer);

			}



			++n_hsp;