Commit 82628433b3583ec0be310c4ff1d62da6068584c5 - diamond-aligner

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README.md less more

32	32	About
33	33	=====
34	34	DIAMOND is currently developed by Benjamin Buchfink at the Drost lab, Max
35		Planck Institute for Developmental Biology, Tübingen, Germany (since 2019).
	35	Planck Institute for Biology, Tübingen, Germany (since 2019).
36	36	Its development was supported for one year by the German Federal Ministry
37	37	for Economic Affairs and Energy through an EXIST grant in 2018-2019. It was
38	38	developed independently by Benjamin Buchfink from 2016-2018. Its initial

43	43	\[[Twitter](https://twitter.com/bbuchfink)\] \[[Google
44	44	Scholar](https://scholar.google.de/citations?user=kjPIF1cAAAAJ)\]
45	45	\[[Drost lab](https://drostlab.com/)\]
46		\[[MPI-EBIO](http://eb.tuebingen.mpg.de/)\]
	46	\[[MPI-BIO](http://eb.tuebingen.mpg.de/)\]
47	47
48	48	When using the tool in published research, please cite:
49	49

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src/ChangeLog less more

	0	[2.0.15]
	1	- Fixed a bug (present since v2.0.12) that caused the `diamond view` workflow to
	2	report a zero bit score for all alignments.
	3
0	4	[2.0.14]
1	5	- Fixed a compiler error on Linux systems that do not define `_SC_LEVEL3_CACHE_SIZE`.
2	6	- Fixed an error when using `--unal 1` with the `cigar` output field.

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src/align/align.h less more

53	53	QueryMapper(query_id, begin, end, cfg)
54	54	{}
55	55	virtual void run(Statistics &stat) override;
56		virtual ~Pipeline() {}
57	56	};
58	57	}
59	58	namespace BandedSwipe {

71	70	DpStat &dp_stat;
72	71	};
73	72	}
74		}⏎
	73	}

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src/basic/basic.cpp less more

28	28	#include "../util/util.h"
29	29	#include "../stats/standard_matrix.h"
30	30
31		const char* Const::version_string = "2.0.14";
	31	const char* Const::version_string = "2.0.15";
32	32	const char* Const::program_name = "diamond";
33	33
34	34	Align_mode::Align_mode(unsigned mode) :

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src/basic/const.h less more

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src/output/daa/daa_file.h less more

15	15	along with this program. If not, see <http://www.gnu.org/licenses/>.
16	16	****/
17	17
18		#ifndef DAA_FILE_H_
19		#define DAA_FILE_H_
20
	18	#pragma once
21	19	#include <string>
22	20	#include <exception>
23	21	#include "../util/ptr_vector.h"

27	25	#include "../util/io/input_file.h"
28	26	#include "../basic/value.h"
29	27	#include "../data/reference.h"
30
31		using std::string;
32	28
33	29	struct DAA_header1
34	30	{

221	217	vector<uint32_t> ref_len_;
222	218
223	219	};
224
225		#endif /* DAA_FILE_H_ */

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src/output/daa/daa_record.cpp less more

76	76	}
77	77	r.context().parse();
78	78	r.evalue = score_matrix.evalue(r.score, r.parent_.context[0].size(), r.subject_len);
	79	r.bit_score = score_matrix.bitscore(r.score);
79	80	return it;
80	81	}⏎

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src/output/daa/daa_record.h less more

15	15	along with this program. If not, see <http://www.gnu.org/licenses/>.
16	16	****/
17	17
18		#ifndef DAA_RECORD_H_
19		#define DAA_RECORD_H_
20
	18	#pragma once
21	19	#include <limits>
22	20	#include "daa_file.h"
23	21	#include "../basic/packed_sequence.h"

27	25	#include "../stats/score_matrix.h"
28	26	#include "../basic/match.h"
29	27
30		using std::string;
31		using std::vector;
32
33		/void translate_query(const vector<Letter>& query, vector<Letter> context)
34		{
35		context[0] = query;
36		context[1] = Translator::reverse(query);
37		}*/
38
39		inline void translate_query(const vector<Letter>& query, vector<Letter> *context)
	28	inline void translate_query(const std::vector<Letter>& query, std::vector<Letter> *context)
40	29	{
41	30	Translator::translate(query, context);
42	31	}

125	114	return align_mode.query_translated ? source_seq.size() : context[0].size();
126	115	}
127	116
128		string query_name;
	117	std::string query_name;
129	118	size_t query_num;
130		vector<Letter> source_seq;
131		vector<Letter> context[6];
	119	std::vector<Letter> source_seq;
	120	std::vector<Letter> context[6];
132	121	TranslatedSequence query_seq;
133	122
134	123	private:

142	131
143	132	};
144	133
145		BinaryBuffer::Iterator& operator>>(BinaryBuffer::Iterator &it, DAA_query_record::Match &r);
146
147		#endif /* DAA_RECORD_H_ */
	134	BinaryBuffer::Iterator& operator>>(BinaryBuffer::Iterator &it, DAA_query_record::Match &r);⏎

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src/test/test_cases.cpp less more