Merge branch 'master' of https://github.com/bbuchfink/diamond

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/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;
 		};
 	}
-}
+}

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 @@ struct DAA_file
 	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;
 }

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 @@ struct DAA_query_record
 
 };
 
-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);