[med-svn] [Git][med-team/diamond-aligner][upstream] New upstream version 2.0.15
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon May 2 12:47:15 BST 2022
Andreas Tille pushed to branch upstream at Debian Med / diamond-aligner
Commits:
82628433 by Andreas Tille at 2022-05-02T12:17:11+02:00
New upstream version 2.0.15
- - - - -
9 changed files:
- README.md
- src/ChangeLog
- src/align/align.h
- src/basic/basic.cpp
- src/basic/const.h
- src/output/daa/daa_file.h
- src/output/daa/daa_record.cpp
- src/output/daa/daa_record.h
- src/test/test_cases.cpp
Changes:
=====================================
README.md
=====================================
@@ -33,7 +33,7 @@ Diamond is actively supported and developed software. Please use the [issue trac
About
=====
DIAMOND is currently developed by Benjamin Buchfink at the Drost lab, Max
-Planck Institute for Developmental Biology, Tübingen, Germany (since 2019).
+Planck Institute for Biology, Tübingen, Germany (since 2019).
Its development was supported for one year by the German Federal Ministry
for Economic Affairs and Energy through an EXIST grant in 2018-2019. It was
developed independently by Benjamin Buchfink from 2016-2018. Its initial
@@ -44,7 +44,7 @@ of Tübingen, Germany.
\[[Twitter](https://twitter.com/bbuchfink)\] \[[Google
Scholar](https://scholar.google.de/citations?user=kjPIF1cAAAAJ)\]
\[[Drost lab](https://drostlab.com/)\]
-\[[MPI-EBIO](http://eb.tuebingen.mpg.de/)\]
+\[[MPI-BIO](http://eb.tuebingen.mpg.de/)\]
**When using the tool in published research, please cite:**
=====================================
src/ChangeLog
=====================================
@@ -1,3 +1,7 @@
+[2.0.15]
+- Fixed a bug (present since v2.0.12) that caused the `diamond view` workflow to
+ report a zero bit score for all alignments.
+
[2.0.14]
- Fixed a compiler error on Linux systems that do not define `_SC_LEVEL3_CACHE_SIZE`.
- Fixed an error when using `--unal 1` with the `cigar` output field.
=====================================
src/align/align.h
=====================================
@@ -54,7 +54,6 @@ namespace ExtensionPipeline {
QueryMapper(query_id, begin, end, cfg)
{}
virtual void run(Statistics &stat) override;
- virtual ~Pipeline() {}
};
}
namespace BandedSwipe {
@@ -72,4 +71,4 @@ namespace ExtensionPipeline {
DpStat &dp_stat;
};
}
-}
\ No newline at end of file
+}
=====================================
src/basic/basic.cpp
=====================================
@@ -29,7 +29,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
#include "../util/util.h"
#include "../stats/standard_matrix.h"
-const char* Const::version_string = "2.0.14";
+const char* Const::version_string = "2.0.15";
const char* Const::program_name = "diamond";
Align_mode::Align_mode(unsigned mode) :
=====================================
src/basic/const.h
=====================================
@@ -25,7 +25,7 @@ struct Const
{
enum {
- build_version = 152,
+ build_version = 153,
#ifdef SINGLE_THREADED
seedp_bits = 0,
#else
=====================================
src/output/daa/daa_file.h
=====================================
@@ -16,9 +16,7 @@ You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
****/
-#ifndef DAA_FILE_H_
-#define DAA_FILE_H_
-
+#pragma once
#include <string>
#include <exception>
#include "../util/ptr_vector.h"
@@ -29,8 +27,6 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
#include "../basic/value.h"
#include "../data/reference.h"
-using std::string;
-
struct DAA_header1
{
enum { VERSION = 1, COMPATIBILITY_VERSION = 0 };
@@ -222,5 +218,3 @@ private:
vector<uint32_t> ref_len_;
};
-
-#endif /* DAA_FILE_H_ */
=====================================
src/output/daa/daa_record.cpp
=====================================
@@ -77,5 +77,6 @@ BinaryBuffer::Iterator& operator>>(BinaryBuffer::Iterator &it, DAA_query_record:
}
r.context().parse();
r.evalue = score_matrix.evalue(r.score, r.parent_.context[0].size(), r.subject_len);
+ r.bit_score = score_matrix.bitscore(r.score);
return it;
}
\ No newline at end of file
=====================================
src/output/daa/daa_record.h
=====================================
@@ -16,9 +16,7 @@ You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
****/
-#ifndef DAA_RECORD_H_
-#define DAA_RECORD_H_
-
+#pragma once
#include <limits>
#include "daa_file.h"
#include "../basic/packed_sequence.h"
@@ -28,16 +26,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
#include "../stats/score_matrix.h"
#include "../basic/match.h"
-using std::string;
-using std::vector;
-
-/*void translate_query(const vector<Letter>& query, vector<Letter> *context)
-{
- context[0] = query;
- context[1] = Translator::reverse(query);
-}*/
-
-inline void translate_query(const vector<Letter>& query, vector<Letter> *context)
+inline void translate_query(const std::vector<Letter>& query, std::vector<Letter> *context)
{
Translator::translate(query, context);
}
@@ -126,10 +115,10 @@ struct DAA_query_record
return align_mode.query_translated ? source_seq.size() : context[0].size();
}
- string query_name;
+ std::string query_name;
size_t query_num;
- vector<Letter> source_seq;
- vector<Letter> context[6];
+ std::vector<Letter> source_seq;
+ std::vector<Letter> context[6];
TranslatedSequence query_seq;
private:
@@ -143,6 +132,4 @@ private:
};
-BinaryBuffer::Iterator& operator>>(BinaryBuffer::Iterator &it, DAA_query_record::Match &r);
-
-#endif /* DAA_RECORD_H_ */
+BinaryBuffer::Iterator& operator>>(BinaryBuffer::Iterator &it, DAA_query_record::Match &r);
\ No newline at end of file
=====================================
src/test/test_cases.cpp
=====================================
@@ -66,7 +66,7 @@ const vector<uint64_t> ref_hashes = {
0xe787dcb23cc5b120,
0x5aa4baf48a888be9,
0xa2519e06e3bfa2fd,
-0xc393e16a2f782562,
+0xe2781c840d096a80,
0x67b3a14cdd541dc3,
};
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/commit/82628433b3583ec0be310c4ff1d62da6068584c5
--
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/commit/82628433b3583ec0be310c4ff1d62da6068584c5
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220502/80e0d046/attachment-0001.htm>
More information about the debian-med-commit
mailing list