Codebase list diamond-aligner / d1f92e8
Rediff patches, dropping two applied upstream. Drop multi_arch: applied upstream Drop fix_i386_and_s390x: applied upstream Ryan Pavlik 4 years ago
5 changed file(s) with 18 addition(s) and 152 deletion(s). Raw diff Collapse all Expand all
+3
-2
debian/patches/82feea2aee5c82e283704b9317cb5e8abc625f90.patch less more
0 From 82feea2aee5c82e283704b9317cb5e8abc625f90 Mon Sep 17 00:00:00 2001
10 From: Benjamin Buchfink <buchfink@gmail.com>
21 Date: Thu, 1 Aug 2019 14:36:14 +0200
32 Subject: [PATCH] Fixed #295.
65 src/dp/needleman_wunsch.cpp | 2 +-
76 1 file changed, 1 insertion(+), 1 deletion(-)
87
8 diff --git a/src/dp/needleman_wunsch.cpp b/src/dp/needleman_wunsch.cpp
9 index 6a12de1..fa96ba0 100644
910 --- a/src/dp/needleman_wunsch.cpp
1011 +++ b/src/dp/needleman_wunsch.cpp
11 @@ -167,7 +167,7 @@ const Fixed_score_buffer<_score>& needle
12 @@ -167,7 +167,7 @@ const Fixed_score_buffer<_score>& needleman_wunsch(sequence query, sequence subj
1213 return mtx.score_buffer();
1314 }
1415
+15
-6
debian/patches/avoid_unwanted_optimisation.patch less more
0 Author: Frédéric Bonnard <frediz@linux.vnet.ibm.com>
0 From: =?utf-8?b?RnLDqWTDqXJpYyBCb25uYXJk?= <frediz@linux.vnet.ibm.com>
1 Date: Fri, 27 Mar 2020 09:50:23 -0500
2 Subject: Force the symbol with c++ explicit function template instantiation
3 for the latter
4
15 Bug-Debian: https://bugs.debian.org/865132
26 Last-Update: Fri, 20 Mar 2020 19:38:49 +0100
3 Description: Force the symbol with c++ explicit function template instantiation for the latter
4 prototype instead of relying on implicit instantiation in needleman_wunsch.cpp
5 .
6 Hint: This is now just a comment since it might be unnecessary.
77
8 prototype instead of relying on implicit instantiation in needleman_wunsch.cpp
9
10 Hint: This is now just a comment since it might be unnecessary.
11 ---
12 src/dp/needleman_wunsch.cpp | 5 ++++-
13 1 file changed, 4 insertions(+), 1 deletion(-)
14
15 diff --git a/src/dp/needleman_wunsch.cpp b/src/dp/needleman_wunsch.cpp
16 index d452cf1..6a12de1 100644
817 --- a/src/dp/needleman_wunsch.cpp
918 +++ b/src/dp/needleman_wunsch.cpp
10 @@ -216,4 +216,7 @@ void smith_waterman(sequence q, sequence
19 @@ -216,4 +216,7 @@ void smith_waterman(sequence q, sequence s, Hsp &out)
1120 out.query_source_range = out.query_range;
1221 out.transcript.reverse();
1322 out.transcript.push_terminator();
+0
-22
debian/patches/fix_i386_and_s390x less more
0 From: Benjamin Buchfink <buchfink@gmail.com>
1 Date: Mon, 17 Feb 2020 13:51:26 +0100
2 Subject: [PATCH] Fixed #324
3 Forwarded: https://github.com/bbuchfink/diamond/commit/aea535c07e09fd41c5ab48ae72b6901d01d8decb
4 --- a/src/util/string/string.h
5 +++ b/src/util/string/string.h
6 @@ -41,6 +41,15 @@ inline std::vector<const char*> charp_ar
7 return v;
8 }
9
10 +template<typename _it>
11 +inline std::vector<const char*> charp_array(_it begin, _it end) {
12 + std::vector<const char*> v;
13 + v.reserve(end - begin);
14 + for (auto i = begin; i != end; ++i)
15 + v.push_back(i->c_str());
16 + return v;
17 +}
18 +
19 #define MAX_LEN(A) max_len(A, sizeof(A)/sizeof(A[0]))
20
21 std::string convert_size(size_t size);
+0
-120
debian/patches/multi_arch less more
0 From: Michael R. Crusoe <michael.crusoe@gmail.com>
1 Subject: handle non-x86 builds again
2 Forwarded: https://github.com/bbuchfink/diamond/pull/323
3 --- a/CMakeLists.txt
4 +++ b/CMakeLists.txt
5 @@ -66,6 +66,104 @@ set(DISPATCH_OBJECTS
6 "src/dp/swipe/swipe_wrapper.cpp"
7 "src/util/tantan.cpp"
8 )
9 +else()
10 +add_executable(diamond $<TARGET_OBJECTS:arch_generic>
11 + src/run/main.cpp
12 + src/basic/config.cpp
13 + src/basic/score_matrix.cpp
14 + src/blast/blast_filter.cpp
15 + src/blast/blast_seg.cpp
16 + src/blast/sm_blosum45.c
17 + src/blast/sm_blosum50.c
18 + src/blast/sm_blosum62.c
19 + src/blast/sm_blosum80.c
20 + src/blast/sm_blosum90.c
21 + src/blast/sm_pam30.c
22 + src/blast/sm_pam70.c
23 + src/blast/sm_pam250.c
24 + src/data/queries.cpp
25 + src/data/reference.cpp
26 + src/data/seed_histogram.cpp
27 + src/output/daa_record.cpp
28 + src/util/command_line_parser.cpp
29 + src/util/seq_file_format.cpp
30 + src/util/util.cpp
31 + src/basic/basic.cpp
32 + src/basic/hssp.cpp
33 + src/dp/ungapped_align.cpp
34 + src/run/tools.cpp
35 + src/dp/greedy_align.cpp
36 + src/output/output_format.cpp
37 + src/output/join_blocks.cpp
38 + src/data/frequent_seeds.cpp
39 + src/align/legacy/query_mapper.cpp
40 + src/output/blast_tab_format.cpp
41 + src/dp/padded_banded_sw.cpp
42 + src/dp/needleman_wunsch.cpp
43 + src/output/blast_pairwise_format.cpp
44 + src/dp/comp_based_stats.cpp
45 + src/run/double_indexed.cpp
46 + src/output/sam_format.cpp
47 + src/align/align.cpp
48 + src/search/setup.cpp
49 + src/dp/diag_scores.cpp
50 + src/data/taxonomy.cpp
51 + src/basic/masking.cpp
52 + src/dp/banded_sw.cpp
53 + src/data/seed_set.cpp
54 + src/util/simd.cpp
55 + src/output/taxon_format.cpp
56 + src/output/view.cpp
57 + src/output/output_sink.cpp
58 + src/output/target_culling.cpp
59 + src/align/legacy/greedy_pipeline.cpp
60 + src/align/legacy/swipe_pipeline.cpp
61 + src/align/legacy/banded_swipe_pipeline.cpp
62 + src/data/ref_dictionary.cpp
63 + src/util/io/compressed_stream.cpp
64 + src/util/io/deserializer.cpp
65 + src/util/io/file_sink.cpp
66 + src/util/io/file_source.cpp
67 + src/util/io/input_file.cpp
68 + src/util/io/input_stream_buffer.cpp
69 + src/util/io/output_file.cpp
70 + src/util/io/output_stream_buffer.cpp
71 + src/util/io/serializer.cpp
72 + src/util/io/temp_file.cpp
73 + src/util/io/text_input_file.cpp
74 + src/data/taxon_list.cpp
75 + src/data/taxonomy_nodes.cpp
76 + src/util/algo/MurmurHash3.cpp
77 + src/search/stage0.cpp
78 + src/data/seed_array.cpp
79 + src/output/paf_format.cpp
80 + src/util/system/system.cpp
81 + src/run/cluster.cpp
82 + src/util/algo/greedy_vortex_cover.cpp
83 + src/util/sequence/sequence.cpp
84 + src/tools/tsv_record.cpp
85 + src/tools/tools.cpp
86 + src/util/system/getRSS.cpp
87 + src/util/math/sparse_matrix.cpp
88 + src/lib/tantan/LambdaCalculator.cc
89 + src/data/taxonomy_filter.cpp
90 + src/util/algo/upgma.cpp
91 + src/util/algo/upgma_mc.cpp
92 + src/util/algo/edge_vec.cpp
93 + src/util/string/string.cpp
94 + src/align/extend.cpp
95 + src/align/target.cpp
96 + src/test/simulate.cpp
97 + src/test/test.cpp
98 + src/align/ranking.cpp
99 + src/align/ungapped.cpp
100 + src/align/gapped.cpp
101 + src/align/culling.cpp
102 + src/cluster/medoid.cpp
103 + src/align/output.cpp
104 + src/tools/roc.cpp
105 +)
106 +endif()
107
108 add_library(arch_generic OBJECT ${DISPATCH_OBJECTS})
109 target_compile_options(arch_generic PUBLIC -DDISPATCH_ARCH=ARCH_GENERIC)
110 --- a/src/tools/benchmark.cpp
111 +++ b/src/tools/benchmark.cpp
112 @@ -136,6 +136,7 @@ void benchmark_ungapped(const sequence &
113
114 cout << "Scalar ungapped extension:\t" << (double)time_span.count() / (n*64) * 1000 << " ps/Cell" << endl;
115 }
116 +#endif
117
118 #ifdef __SSSE3__
119 void benchmark_ssse3_shuffle(const sequence &s1, const sequence &s2)
+0
-2
debian/patches/series less more
00 avoid_unwanted_optimisation.patch
11 82feea2aee5c82e283704b9317cb5e8abc625f90.patch
2 multi_arch
3 fix_i386_and_s390x