[med-svn] [Git][med-team/diamond-aligner][master] Rediff patches, dropping two applied upstream.
Andreas Tille
gitlab at salsa.debian.org
Fri Mar 27 15:11:21 GMT 2020
Andreas Tille pushed to branch master at Debian Med / diamond-aligner
Commits:
d1f92e86 by Ryan Pavlik at 2020-03-27T10:03:56-05:00
Rediff patches, dropping two applied upstream.
Drop multi_arch: applied upstream
Drop fix_i386_and_s390x: applied upstream
- - - - -
5 changed files:
- debian/patches/82feea2aee5c82e283704b9317cb5e8abc625f90.patch
- debian/patches/avoid_unwanted_optimisation.patch
- − debian/patches/fix_i386_and_s390x
- − debian/patches/multi_arch
- debian/patches/series
Changes:
=====================================
debian/patches/82feea2aee5c82e283704b9317cb5e8abc625f90.patch
=====================================
@@ -1,4 +1,3 @@
-From 82feea2aee5c82e283704b9317cb5e8abc625f90 Mon Sep 17 00:00:00 2001
From: Benjamin Buchfink <buchfink at gmail.com>
Date: Thu, 1 Aug 2019 14:36:14 +0200
Subject: [PATCH] Fixed #295.
@@ -7,9 +6,11 @@ Subject: [PATCH] Fixed #295.
src/dp/needleman_wunsch.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
+diff --git a/src/dp/needleman_wunsch.cpp b/src/dp/needleman_wunsch.cpp
+index 6a12de1..fa96ba0 100644
--- a/src/dp/needleman_wunsch.cpp
+++ b/src/dp/needleman_wunsch.cpp
-@@ -167,7 +167,7 @@ const Fixed_score_buffer<_score>& needle
+@@ -167,7 +167,7 @@ const Fixed_score_buffer<_score>& needleman_wunsch(sequence query, sequence subj
return mtx.score_buffer();
}
=====================================
debian/patches/avoid_unwanted_optimisation.patch
=====================================
@@ -1,14 +1,23 @@
-Author: Frédéric Bonnard <frediz at linux.vnet.ibm.com>
+From: =?utf-8?b?RnLDqWTDqXJpYyBCb25uYXJk?= <frediz at linux.vnet.ibm.com>
+Date: Fri, 27 Mar 2020 09:50:23 -0500
+Subject: Force the symbol with c++ explicit function template instantiation
+ for the latter
+
Bug-Debian: https://bugs.debian.org/865132
Last-Update: Fri, 20 Mar 2020 19:38:49 +0100
-Description: Force the symbol with c++ explicit function template instantiation for the latter
- prototype instead of relying on implicit instantiation in needleman_wunsch.cpp
- .
- Hint: This is now just a comment since it might be unnecessary.
+ prototype instead of relying on implicit instantiation in needleman_wunsch.cpp
+
+Hint: This is now just a comment since it might be unnecessary.
+---
+ src/dp/needleman_wunsch.cpp | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/src/dp/needleman_wunsch.cpp b/src/dp/needleman_wunsch.cpp
+index d452cf1..6a12de1 100644
--- a/src/dp/needleman_wunsch.cpp
+++ b/src/dp/needleman_wunsch.cpp
-@@ -216,4 +216,7 @@ void smith_waterman(sequence q, sequence
+@@ -216,4 +216,7 @@ void smith_waterman(sequence q, sequence s, Hsp &out)
out.query_source_range = out.query_range;
out.transcript.reverse();
out.transcript.push_terminator();
=====================================
debian/patches/fix_i386_and_s390x deleted
=====================================
@@ -1,22 +0,0 @@
-From: Benjamin Buchfink <buchfink at gmail.com>
-Date: Mon, 17 Feb 2020 13:51:26 +0100
-Subject: [PATCH] Fixed #324
-Forwarded: https://github.com/bbuchfink/diamond/commit/aea535c07e09fd41c5ab48ae72b6901d01d8decb
---- a/src/util/string/string.h
-+++ b/src/util/string/string.h
-@@ -41,6 +41,15 @@ inline std::vector<const char*> charp_ar
- return v;
- }
-
-+template<typename _it>
-+inline std::vector<const char*> charp_array(_it begin, _it end) {
-+ std::vector<const char*> v;
-+ v.reserve(end - begin);
-+ for (auto i = begin; i != end; ++i)
-+ v.push_back(i->c_str());
-+ return v;
-+}
-+
- #define MAX_LEN(A) max_len(A, sizeof(A)/sizeof(A[0]))
-
- std::string convert_size(size_t size);
=====================================
debian/patches/multi_arch deleted
=====================================
@@ -1,120 +0,0 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
-Subject: handle non-x86 builds again
-Forwarded: https://github.com/bbuchfink/diamond/pull/323
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -66,6 +66,104 @@ set(DISPATCH_OBJECTS
- "src/dp/swipe/swipe_wrapper.cpp"
- "src/util/tantan.cpp"
- )
-+else()
-+add_executable(diamond $<TARGET_OBJECTS:arch_generic>
-+ src/run/main.cpp
-+ src/basic/config.cpp
-+ src/basic/score_matrix.cpp
-+ src/blast/blast_filter.cpp
-+ src/blast/blast_seg.cpp
-+ src/blast/sm_blosum45.c
-+ src/blast/sm_blosum50.c
-+ src/blast/sm_blosum62.c
-+ src/blast/sm_blosum80.c
-+ src/blast/sm_blosum90.c
-+ src/blast/sm_pam30.c
-+ src/blast/sm_pam70.c
-+ src/blast/sm_pam250.c
-+ src/data/queries.cpp
-+ src/data/reference.cpp
-+ src/data/seed_histogram.cpp
-+ src/output/daa_record.cpp
-+ src/util/command_line_parser.cpp
-+ src/util/seq_file_format.cpp
-+ src/util/util.cpp
-+ src/basic/basic.cpp
-+ src/basic/hssp.cpp
-+ src/dp/ungapped_align.cpp
-+ src/run/tools.cpp
-+ src/dp/greedy_align.cpp
-+ src/output/output_format.cpp
-+ src/output/join_blocks.cpp
-+ src/data/frequent_seeds.cpp
-+ src/align/legacy/query_mapper.cpp
-+ src/output/blast_tab_format.cpp
-+ src/dp/padded_banded_sw.cpp
-+ src/dp/needleman_wunsch.cpp
-+ src/output/blast_pairwise_format.cpp
-+ src/dp/comp_based_stats.cpp
-+ src/run/double_indexed.cpp
-+ src/output/sam_format.cpp
-+ src/align/align.cpp
-+ src/search/setup.cpp
-+ src/dp/diag_scores.cpp
-+ src/data/taxonomy.cpp
-+ src/basic/masking.cpp
-+ src/dp/banded_sw.cpp
-+ src/data/seed_set.cpp
-+ src/util/simd.cpp
-+ src/output/taxon_format.cpp
-+ src/output/view.cpp
-+ src/output/output_sink.cpp
-+ src/output/target_culling.cpp
-+ src/align/legacy/greedy_pipeline.cpp
-+ src/align/legacy/swipe_pipeline.cpp
-+ src/align/legacy/banded_swipe_pipeline.cpp
-+ src/data/ref_dictionary.cpp
-+ src/util/io/compressed_stream.cpp
-+ src/util/io/deserializer.cpp
-+ src/util/io/file_sink.cpp
-+ src/util/io/file_source.cpp
-+ src/util/io/input_file.cpp
-+ src/util/io/input_stream_buffer.cpp
-+ src/util/io/output_file.cpp
-+ src/util/io/output_stream_buffer.cpp
-+ src/util/io/serializer.cpp
-+ src/util/io/temp_file.cpp
-+ src/util/io/text_input_file.cpp
-+ src/data/taxon_list.cpp
-+ src/data/taxonomy_nodes.cpp
-+ src/util/algo/MurmurHash3.cpp
-+ src/search/stage0.cpp
-+ src/data/seed_array.cpp
-+ src/output/paf_format.cpp
-+ src/util/system/system.cpp
-+ src/run/cluster.cpp
-+ src/util/algo/greedy_vortex_cover.cpp
-+ src/util/sequence/sequence.cpp
-+ src/tools/tsv_record.cpp
-+ src/tools/tools.cpp
-+ src/util/system/getRSS.cpp
-+ src/util/math/sparse_matrix.cpp
-+ src/lib/tantan/LambdaCalculator.cc
-+ src/data/taxonomy_filter.cpp
-+ src/util/algo/upgma.cpp
-+ src/util/algo/upgma_mc.cpp
-+ src/util/algo/edge_vec.cpp
-+ src/util/string/string.cpp
-+ src/align/extend.cpp
-+ src/align/target.cpp
-+ src/test/simulate.cpp
-+ src/test/test.cpp
-+ src/align/ranking.cpp
-+ src/align/ungapped.cpp
-+ src/align/gapped.cpp
-+ src/align/culling.cpp
-+ src/cluster/medoid.cpp
-+ src/align/output.cpp
-+ src/tools/roc.cpp
-+)
-+endif()
-
- add_library(arch_generic OBJECT ${DISPATCH_OBJECTS})
- target_compile_options(arch_generic PUBLIC -DDISPATCH_ARCH=ARCH_GENERIC)
---- a/src/tools/benchmark.cpp
-+++ b/src/tools/benchmark.cpp
-@@ -136,6 +136,7 @@ void benchmark_ungapped(const sequence &
-
- cout << "Scalar ungapped extension:\t" << (double)time_span.count() / (n*64) * 1000 << " ps/Cell" << endl;
- }
-+#endif
-
- #ifdef __SSSE3__
- void benchmark_ssse3_shuffle(const sequence &s1, const sequence &s2)
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,2 @@
avoid_unwanted_optimisation.patch
82feea2aee5c82e283704b9317cb5e8abc625f90.patch
-multi_arch
-fix_i386_and_s390x
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/commit/d1f92e86ffb674af792d5f60093c8d08bf1fda11
--
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/commit/d1f92e86ffb674af792d5f60093c8d08bf1fda11
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