[med-svn] [Git][med-team/vg][master] 2 commits: Rebase quilt patches for vg 1.78.0+ds
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Oct 21 15:59:11 BST 2026
Andreas Tille pushed to branch master at Debian Med / vg
Commits:
2a68633c by Andreas Tille at 2026-10-21T16:37:34+02:00
Rebase quilt patches for vg 1.78.0+ds
Refresh all remaining patches to apply cleanly against the new
upstream 1.78.0+ds source tree, and drop patches that are now obsolete
(already upstream or for removed dependencies):
* Drop gcc-12, no_need_for_snappy, use_packaged_fermi-lite,
libVCFH_unneeded, better_clean, avoid_abs_confusion
* Refresh use_packaged_* patches for the new Makefile, drop the
now-obsolete source_me.sh hunk from crossbuild, and add
Assisted-By trailers
- - - - -
9b5c9d6b by Andreas Tille at 2026-10-21T16:57:07+02:00
Deactivate quilt patches that patch bundled deps/
The vg source tarball does not ship deps/ (all dependencies are expected
to come from Debian packages). Deactivate patches whose hunks only
modify files under deps/, and trim the mixed patches to their non-deps
(use-packaged-dependency) changes:
* Deactivate (comment out in series): no_pg, hardening_flags,
use_packaged_lz4, parallize_better, crossbuild, python3
* Trim simde to the Makefile and src/preflight* portability changes
(use of packaged libsimde-dev)
* Trim use_packaged_libtsl-hopscotch-map-dev to the Makefile change
(use of packaged libtsl-hopscotch-map-dev)
- - - - -
22 changed files:
- − debian/patches/avoid_abs_confusion
- − debian/patches/better_clean
- debian/patches/crossbuild
- − debian/patches/gcc-12
- debian/patches/hardening_flags
- − debian/patches/libVCFH_unneeded
- − debian/patches/no_need_for_snappy
- debian/patches/no_rpath
- debian/patches/series
- debian/patches/simde
- debian/patches/static
- debian/patches/use_packaged_elfutils
- debian/patches/use_packaged_fastahack
- − debian/patches/use_packaged_fermi-lite
- debian/patches/use_packaged_htslib
- debian/patches/use_packaged_jemalloc
- debian/patches/use_packaged_libbackward-cpp
- debian/patches/use_packaged_libdeflate
- debian/patches/use_packaged_libtsl-hopscotch-map-dev
- debian/patches/use_packaged_raptor2
- debian/patches/use_packaged_sparsehash
- debian/patches/use_packaged_vcflib
Changes:
=====================================
debian/patches/avoid_abs_confusion deleted
=====================================
@@ -1,70 +0,0 @@
-From: Bastian Germann <bage at debian.org>
-Date: Fri, 1 Nov 2024 16:26:50 +0100
-Subject: Avoid compiler confusion on overloaded abs
----
-diff --git a/src/multipath_alignment_graph.cpp b/src/multipath_alignment_graph.cpp
-index 0d0a249..aeb1327 100644
---- a/src/multipath_alignment_graph.cpp
-+++ b/src/multipath_alignment_graph.cpp
-@@ -6417,7 +6417,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
- for (const auto& path_node : path_nodes) {
- for (const auto& edge : path_node.edges) {
- const auto& next_node = path_nodes[edge.first];
-- shift = max<size_t>(shift, abs<int64_t>((next_node.begin - path_node.end) - edge.second));
-+ shift = max<size_t>(shift, llabs((next_node.begin - path_node.end) - edge.second));
- }
- }
- return shift;
-@@ -6441,7 +6441,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
- ++in_degree[edge.first];
-
- const auto& next_node = path_nodes[edge.first];
-- size_t shift = abs<int64_t>((next_node.begin - path_node.end) - edge.second);
-+ size_t shift = llabs((next_node.begin - path_node.end) - edge.second);
-
- #ifdef debug_shift_pruning
- cerr << "shift DP reverse " << i << " <- " << edge.first << " with shift " << shift << " for total " << min_shift_rev[edge.first] + shift << endl;
-@@ -6467,7 +6467,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
- else {
- for (auto& edge : path_node.edges) {
- const auto& next_node = path_nodes[edge.first];
-- size_t shift = abs<int64_t>((next_node.begin - path_node.end) - edge.second);
-+ size_t shift = llabs((next_node.begin - path_node.end) - edge.second);
- #ifdef debug_shift_pruning
- cerr << "shift DP forward " << i << " -> " << edge.first << " with shift " << shift << " for total " << min_shift_fwd[i] + shift << endl;
- #endif
-@@ -6489,7 +6489,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
- for (size_t j = 0; j < path_node.edges.size(); ++j) {
- auto& edge = path_node.edges[j];
- const auto& next_node = path_nodes[edge.first];
-- size_t shift = abs<int64_t>((next_node.begin - path_node.end) - edge.second);
-+ size_t shift = llabs((next_node.begin - path_node.end) - edge.second);
-
- size_t min_edge_shift = min_shift_fwd[i] + shift + min_shift_rev[edge.first];
-
-diff --git a/src/multipath_mapper.cpp b/src/multipath_mapper.cpp
-index 23e52a7..7f8c07f 100644
---- a/src/multipath_mapper.cpp
-+++ b/src/multipath_mapper.cpp
-@@ -2446,7 +2446,7 @@ namespace vg {
- // in the left_idxs and right_idxs vectors
- int64_t target_len = 2 * seq_len - left_side.clip_length - right_side.clip_length;
- auto distance_diff = [&](size_t l, size_t r) {
-- return abs<int64_t>(get<2>(left_sites[left_idxs[l]]) + get<2>(right_sites[right_idxs[r]]) - target_len);
-+ return llabs(get<2>(left_sites[left_idxs[l]]) + get<2>(right_sites[right_idxs[r]]) - target_len);
- };
-
- // sweep to identify pairs that most nearly align
-diff --git a/src/subcommand/gampcompare_main.cpp b/src/subcommand/gampcompare_main.cpp
-index fd8b5b4..a6d5c4c 100644
---- a/src/subcommand/gampcompare_main.cpp
-+++ b/src/subcommand/gampcompare_main.cpp
-@@ -218,7 +218,7 @@ int main_gampcompare(int argc, char** argv) {
- if (path_true_positions[i].second == path_mapped_positions[j].second) {
- // there is a pair of positions on the same strand of the same path
- abs_dist = min<int64_t>(abs_dist,
-- abs<int64_t>(path_true_positions[i].first - path_mapped_positions[j].first));
-+ llabs(path_true_positions[i].first - path_mapped_positions[j].first));
- }
- }
- }
=====================================
debian/patches/better_clean deleted
=====================================
@@ -1,30 +0,0 @@
-From: "Michael R. Crusoe" <crusoe at debian.org>
-Date: Sat, 1 Feb 2020 09:07:59 +0100
-Subject: don't clean a file that is part of the distribution tarball
-
-Forwarded: not-needed
----
- Makefile | 3 +--
- 1 file changed, 1 insertion(+), 2 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 891c855..848d221 100644
---- a/Makefile
-+++ b/Makefile
-@@ -894,7 +894,7 @@ clean-vg:
- $(RM) -f $(ALGORITHMS_SHARED_OBJ_DIR)/*.o $(ALGORITHMS_SHARED_OBJ_DIR)/*.d
- $(RM) -f $(IO_OBJ_DIR)/*.o $(IO_OBJ_DIR)/*.d
- $(RM) -f $(IO_SHARED_OBJ_DIR)/*.o $(IO_SHARED_OBJ_DIR)/*.d
-- $(RM) -f $(INC_DIR)/vg_git_version.hpp $(INC_DIR)/vg_system_version.hpp
-+ $(RM) -f $(INC_DIR)/vg_git_version.hpp
-
- clean: clean-vcflib
- $(RM) -r $(UNITTEST_BIN_DIR)
-@@ -910,7 +910,6 @@ clean: clean-vcflib
- $(RM) -r $(CONFIG_OBJ_DIR)
- $(RM) -r $(SHARED_OBJ_DIR)
- $(RM) -r $(OBJ_DIR)
-- $(RM) -r $(INC_DIR)
- $(RM) -r share/
- cd $(DEP_DIR) && cd htslib && $(MAKE) clean
- cd $(DEP_DIR) && cd tabixpp && rm -f tabix.o libtabixpp.a
=====================================
debian/patches/crossbuild
=====================================
@@ -7,14 +7,13 @@ Forwarded: https://github.com/yoheirosen/sublinear-Li-Stephens/pull/7
Forwarded: https://github.com/benedictpaten/sonLib/pull/42
Forwarded: https://github.com/vgteam/cpp_progress_bar/pull/2
Forwarded: https://github.com/vgteam/gfakluge/pull/6
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
deps/progress_bar/makefile | 11 ++++-------
deps/sonLib/include.mk | 3 ++-
source_me.sh | 4 ++--
3 files changed, 8 insertions(+), 10 deletions(-)
-diff --git a/deps/progress_bar/makefile b/deps/progress_bar/makefile
-index 3d5d8d7..2ab06c1 100644
--- a/deps/progress_bar/makefile
+++ b/deps/progress_bar/makefile
@@ -1,4 +1,4 @@
@@ -43,8 +42,6 @@ index 3d5d8d7..2ab06c1 100644
clean :
@rm -rf progress_bar $(OBJ)
-diff --git a/deps/sonLib/include.mk b/deps/sonLib/include.mk
-index 8f52bbd..fef4872 100644
--- a/deps/sonLib/include.mk
+++ b/deps/sonLib/include.mk
@@ -3,6 +3,7 @@ HOSTNAME = $(shell hostname)
@@ -64,18 +61,3 @@ index 8f52bbd..fef4872 100644
endif
else
cxx = ${CC} -std=c99
-diff --git a/source_me.sh b/source_me.sh
-index 0bb948c..6a75fd2 100755
---- a/source_me.sh
-+++ b/source_me.sh
-@@ -9,8 +9,8 @@ export LD_INCLUDE_PATH=`pwd`/include:$LD_INCLUDE_PATH
- export CFLAGS="-I $(pwd)/include ${CFLAGS}"
- export CXXFLAGS="-I $(pwd)/include -I$(pwd)/include/dynamic ${CXXFLAGS}"
- export PATH=`pwd`/bin:`pwd`/scripts:"$PATH"
--export CC=$(which gcc)
--export CXX=$(which g++)
-+export CC="${CC:=gcc}"
-+export CXX="${CXX:=g++}"
-
- #
- # disable until file arguments work as in normal bash :(
=====================================
debian/patches/gcc-12 deleted
=====================================
@@ -1,113 +0,0 @@
-From: "Michael R. Crusoe" <crusoe at debian.org>
-Date: Wed, 11 Sep 2024 17:58:38 +0200
-Subject: GCC 12+ fixes
-
-Forwarded: not-needed
-
-Similar to https://github.com/vgteam/vg/commit/fa824c1f5500a71ee215311e18049c46c50712b5
----
- deps/kff-cpp-api/kff_io.cpp | 1 +
- deps/kff-cpp-api/main.cpp | 1 +
- deps/libhandlegraph/src/include/handlegraph/serializable.hpp | 1 +
- .../deps/libhandlegraph/src/include/handlegraph/serializable.hpp | 1 +
- deps/sublinear-Li-Stephens/src/haplotype_manager.hpp | 1 +
- deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp | 3 ++-
- src/multipath_mapper.cpp | 6 ++++--
- 7 files changed, 11 insertions(+), 3 deletions(-)
-
-diff --git a/deps/kff-cpp-api/kff_io.cpp b/deps/kff-cpp-api/kff_io.cpp
-index e23d396..76b4864 100644
---- a/deps/kff-cpp-api/kff_io.cpp
-+++ b/deps/kff-cpp-api/kff_io.cpp
-@@ -2,6 +2,7 @@
- #include <cassert>
- #include <cstring>
- #include <sstream>
-+#include <cstdint>
- #include <math.h>
-
- #include <map>
-diff --git a/deps/kff-cpp-api/main.cpp b/deps/kff-cpp-api/main.cpp
-index bc4cf5c..59c3d0b 100644
---- a/deps/kff-cpp-api/main.cpp
-+++ b/deps/kff-cpp-api/main.cpp
-@@ -3,6 +3,7 @@
- #include <sstream>
- #include <string>
- #include <cstring>
-+#include <cstdint>
- #include <map>
-
- #include "kff_io.hpp"
-diff --git a/deps/libhandlegraph/src/include/handlegraph/serializable.hpp b/deps/libhandlegraph/src/include/handlegraph/serializable.hpp
-index b16a753..a7f6ab8 100644
---- a/deps/libhandlegraph/src/include/handlegraph/serializable.hpp
-+++ b/deps/libhandlegraph/src/include/handlegraph/serializable.hpp
-@@ -8,6 +8,7 @@
- */
-
- #include <iostream>
-+#include <cstdint>
-
- namespace handlegraph {
-
-diff --git a/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/serializable.hpp b/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/serializable.hpp
-index b16a753..a7f6ab8 100644
---- a/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/serializable.hpp
-+++ b/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/serializable.hpp
-@@ -8,6 +8,7 @@
- */
-
- #include <iostream>
-+#include <cstdint>
-
- namespace handlegraph {
-
-diff --git a/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp b/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp
-index aac6d91..eee423e 100644
---- a/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp
-+++ b/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp
-@@ -8,6 +8,7 @@
- #include <vector>
- #include <string>
- #include <iostream>
-+#include <cstdint>
-
- using namespace std;
-
-diff --git a/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp b/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp
-index e4b2283..5ed35a4 100644
---- a/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp
-+++ b/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp
-@@ -4,6 +4,7 @@
- #include "probability.hpp"
- #include "delay_multiplier.hpp"
- #include "haplotype_state_node.hpp"
-+#include <cstdint>
- #include <unordered_set>
-
- using namespace std;
-@@ -39,4 +40,4 @@ public:
- void set_initial_position(size_t position);
- };
-
--#endif
-\ No newline at end of file
-+#endif
-diff --git a/src/multipath_mapper.cpp b/src/multipath_mapper.cpp
-index 23e52a7..fe7aa3b 100644
---- a/src/multipath_mapper.cpp
-+++ b/src/multipath_mapper.cpp
-@@ -1836,8 +1836,10 @@ namespace vg {
- std::swap(rescued_secondaries[i], rescued_secondaries[end - 1]);
- std::swap(rescued_distances[i], rescued_distances[end - 1]);
- std::swap(rescued_multiplicities[i], rescued_multiplicities[end - 1]);
-- std::swap(duplicate[i], duplicate[end - 1]);
--
-+ // nb: cant std::swap bool vectors in new c++
-+ bool dupe_i = duplicate[i];
-+ duplicate[i] = duplicate[end - 1];
-+ duplicate[end - 1] = dupe_i;
- end--;
- }
- else {
=====================================
debian/patches/hardening_flags
=====================================
@@ -10,6 +10,7 @@ https://github.com/vgteam/vg/pull/3168
https://github.com/vgteam/cpp_progress_bar/pull/2
So that Debian can pass hardening flags
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
deps/libvgio/CMakeLists.txt | 2 +-
deps/progress_bar/makefile | 2 +-
@@ -23,12 +24,10 @@ So that Debian can pass hardening flags
deps/xg/deps/gfakluge/Makefile | 6 +--
10 files changed, 36 insertions(+), 43 deletions(-)
-diff --git a/deps/libvgio/CMakeLists.txt b/deps/libvgio/CMakeLists.txt
-index 916cece..9b87406 100644
--- a/deps/libvgio/CMakeLists.txt
+++ b/deps/libvgio/CMakeLists.txt
-@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.10)
- project(libvgio VERSION 0.0.0 LANGUAGES CXX)
+@@ -6,7 +6,7 @@ OPTION(USE_INSTALLED_LIBHANDLEGRAPH_ONLY
+
# Optimize by default, but also include debug info
-set(CMAKE_CXX_FLAGS "-O3 -g ${CMAKE_CXX_FLAGS}")
@@ -36,8 +35,6 @@ index 916cece..9b87406 100644
# Don't allow any -std= flags in
string(REGEX REPLACE " *-std=[^ ]*" "" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
find_package(OpenMP REQUIRED)
-diff --git a/deps/progress_bar/makefile b/deps/progress_bar/makefile
-index 883b1f2..3d5d8d7 100644
--- a/deps/progress_bar/makefile
+++ b/deps/progress_bar/makefile
@@ -1,5 +1,5 @@
@@ -47,11 +44,9 @@ index 883b1f2..3d5d8d7 100644
TARGET = progress_bar
OBJ = main.o progress_bar.o
-diff --git a/deps/sdsl-lite/CMakeLists.txt b/deps/sdsl-lite/CMakeLists.txt
-index 2ec6355..012ad23 100644
--- a/deps/sdsl-lite/CMakeLists.txt
+++ b/deps/sdsl-lite/CMakeLists.txt
-@@ -115,7 +115,6 @@ else()
+@@ -116,7 +116,6 @@ else()
message(WARNING "git not found. Cloning of submodules will not work.")
endif()
@@ -59,24 +54,20 @@ index 2ec6355..012ad23 100644
add_subdirectory(include)
add_subdirectory(lib)
-diff --git a/deps/sdsl-lite/install.sh b/deps/sdsl-lite/install.sh
-index cc5fd40..cfd8779 100755
--- a/deps/sdsl-lite/install.sh
+++ b/deps/sdsl-lite/install.sh
-@@ -92,11 +92,6 @@ echo "The sdsl include files are located in '${SDSL_INSTALL_PREFIX}/include'."
+@@ -101,11 +101,6 @@ echo "The sdsl include files are located
echo "The library files are located in '${SDSL_INSTALL_PREFIX}/lib'."
echo " "
echo "Sample programs can be found in the examples-directory."
-echo "A program 'example.cpp' can be compiled with the command: "
--echo "g++ -std=c++14 -DNDEBUG -O3 [-msse4.2] \\"
+-echo "g++ -std=c++17 -DNDEBUG -O3 [-msse4.2] \\"
-echo " -I${SDSL_INSTALL_PREFIX}/include -L${SDSL_INSTALL_PREFIX}/lib \\"
-echo " example.cpp -lsdsl -ldivsufsort -ldivsufsort64"
-echo " "
echo "Tests in the test-directory"
echo "A cheat sheet in the extras/cheatsheet-directory."
echo "Have fun!"
-diff --git a/deps/sdsl-lite/lib/CMakeLists.txt b/deps/sdsl-lite/lib/CMakeLists.txt
-index b2e606e..8f6e31c 100644
--- a/deps/sdsl-lite/lib/CMakeLists.txt
+++ b/deps/sdsl-lite/lib/CMakeLists.txt
@@ -1,6 +1,5 @@
@@ -86,11 +77,9 @@ index b2e606e..8f6e31c 100644
)
-diff --git a/deps/sdsl-lite/lib/structure_tree.cpp.cmake b/deps/sdsl-lite/lib/structure_tree.cpp.cmake
-index d13879a..861368a 100644
--- a/deps/sdsl-lite/lib/structure_tree.cpp.cmake
+++ b/deps/sdsl-lite/lib/structure_tree.cpp.cmake
-@@ -45,7 +45,7 @@ std::string create_html_header(const char* file_name)
+@@ -45,7 +45,7 @@ std::string create_html_header(const cha
<< " <head>\n"
<< " <meta http-equiv=\"Content-Type\" content=\"text/html;charset=utf-8\">\n"
<< " <title>" << file_name << "</title>\n"
@@ -99,8 +88,6 @@ index d13879a..861368a 100644
<< " <script src=\"http://d3js.org/d3.v2.js\"></script>\n"
<< " <style type=\"text/css\">\n"
<< " path { stroke: #000; stroke-width: 0.8; cursor: pointer; }\n"
-diff --git a/deps/sonLib/C/Makefile b/deps/sonLib/C/Makefile
-index cf83395..e595ad4 100644
--- a/deps/sonLib/C/Makefile
+++ b/deps/sonLib/C/Makefile
@@ -52,8 +52,8 @@ ${libPath}/%.h: inc/%.h
@@ -114,8 +101,6 @@ index cf83395..e595ad4 100644
ar rc sonLib.a *.o ${quickTreeObjects}
ranlib sonLib.a
rm *.o
-diff --git a/deps/sonLib/externalTools/quicktree_1.1/Makefile b/deps/sonLib/externalTools/quicktree_1.1/Makefile
-index 3214626..6059a07 100755
--- a/deps/sonLib/externalTools/quicktree_1.1/Makefile
+++ b/deps/sonLib/externalTools/quicktree_1.1/Makefile
@@ -22,7 +22,7 @@ all: $(BIN)/quicktree
@@ -127,137 +112,6 @@ index 3214626..6059a07 100755
$(OBJ)/quicktree.o : $(SRC)/quicktree.c
$(CC) $(CFLAGS) $(CPPFLAGS) -o $(OBJ)/quicktree.o $(SRC)/quicktree.c
-diff --git a/deps/sublinear-Li-Stephens/makefile b/deps/sublinear-Li-Stephens/makefile
-index d89044e..a8c1788 100644
---- a/deps/sublinear-Li-Stephens/makefile
-+++ b/deps/sublinear-Li-Stephens/makefile
-@@ -9,7 +9,7 @@ LIB_DIR:= $(CWD)/lib
- DEP_DIR:= $(CWD)/deps
-
- CXX:=g++
--CXXFLAGS:=-std=c++11 -g
-+CXXFLAGS += -std=c++11 -g
-
- ifeq ($(INCLUDE_FLAGS),)
- # Include flags may be set by library user
-@@ -42,89 +42,89 @@ clean:
- rm -f $(BIN_DIR)/* $(OBJ_DIR)/*.o $(TEST_OBJ_DIR)/*.o $(LIB_DIR)/*
-
- tests : $(TEST_OBJ_DIR)/test.o $(CORE_OBJ) $(LIBHTS)
-- $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/tests $(LIBS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/tests $(LIBS)
-
- tree_tests : $(TEST_OBJ_DIR)/tree_tests.o $(CORE_OBJ) $(TREE_OBJ) $(LIBHTS)
-- $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/tree_tests $(LIBS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/tree_tests $(LIBS)
-
- speed_tree : $(TEST_OBJ_DIR)/speed_tree.o $(CORE_OBJ) $(TREE_OBJ) $(LIBHTS)
-- $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/speed_tree $(LIBS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/speed_tree $(LIBS)
-
- interface : $(OBJ_DIR)/linhapexample.o $(OBJ_DIR)/interface.o $(CORE_OBJ) $(TREE_OBJ) $(LIBHTS)
-- $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/linhapexample $(LIBS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/linhapexample $(LIBS)
-
- serializer : $(OBJ_DIR)/serialize_index.o $(CORE_OBJ) $(LIBHTS)
-- $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/serializer $(LIBS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/serializer $(LIBS)
-
- profiler : $(OBJ_DIR)/profiler.o $(CORE_OBJ)
-- $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/profiler $(LIBS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/profiler $(LIBS)
-
- $(LIB_DIR)/libsublinearLS.a : $(CORE_OBJ) $(TREE_OBJ)
- ar rc $@ $^
- ranlib $@
-
- $(OBJ_DIR)/allele.o : $(SRC_DIR)/allele.cpp $(SRC_DIR)/allele.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -Wno-error=return-type $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/linhapexample.o : $(SRC_DIR)/linhapexample.c $(SRC_DIR)/interface.h $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
- gcc -std=c11 $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/interface.o : $(SRC_DIR)/interface.cpp $(SRC_DIR)/interface.h $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/haplotype_state_node.o : $(SRC_DIR)/haplotype_state_node.cpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -Wno-error=return-type $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/haplotype_state_tree.o : $(SRC_DIR)/haplotype_state_tree.cpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/haplotype_manager.o : $(SRC_DIR)/haplotype_manager.cpp $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(TEST_OBJ_DIR)/speed_tree.o : $(TEST_SRC_DIR)/speed_tree.cpp $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/delay_multiplier.o : $(SRC_DIR)/delay_multiplier.cpp $(SRC_DIR)/delay_multiplier.hpp $(SRC_DIR)/math.hpp $(SRC_DIR)/DP_map.hpp $(SRC_DIR)/row_set.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/DP_map.o : $(SRC_DIR)/DP_map.cpp $(SRC_DIR)/math.hpp $(SRC_DIR)/DP_map.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/input_haplotype.o : $(SRC_DIR)/input_haplotype.cpp $(SRC_DIR)/input_haplotype.hpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/math.o : $(SRC_DIR)/math.cpp $(SRC_DIR)/math.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/probability.o : $(SRC_DIR)/probability.cpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/penalty_set.o : $(SRC_DIR)/penalty_set.cpp $(SRC_DIR)/penalty_set.hpp $(SRC_DIR)/math.hpp $(SRC_DIR)/DP_map.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/reference.o : $(SRC_DIR)/reference.cpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp $(SRC_DIR)/row_set.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/reference_sequence.o : $(SRC_DIR)/reference_sequence.cpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/row_set.o : $(SRC_DIR)/row_set.cpp $(SRC_DIR)/row_set.hpp $(SRC_DIR)/allele.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/set_of_extensions.o : $(SRC_DIR)/set_of_extensions.cpp $(SRC_DIR)/set_of_extensions.hpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(TEST_OBJ_DIR)/test.o : $(TEST_SRC_DIR)/test.cpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(TEST_OBJ_DIR)/tree_tests.o : $(TEST_SRC_DIR)/tree_tests.cpp $(SRC_DIR)/haplotype_manager.hpp $(SRC_DIR)/reference_sequence.hpp $(SRC_DIR)/set_of_extensions.hpp $(SRC_DIR)/haplotype_state_tree.hpp $(SRC_DIR)/haplotype_state_node.hpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/serialize_index.o : $(SRC_DIR)/serialize_index.cpp $(SRC_DIR)/reference.hpp $(SRC_DIR)/allele.hpp $(SRC_DIR)/row_set.hpp
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(OBJ_DIR)/profiler.o : $(SRC_DIR)/test/profiler.cpp $(PROBABILITY_DEPS)
-- $(CXX) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDE_FLAGS) $(LIBS) -c $< -o $@
-
- $(LIBHTS) :
- cd deps/htslib && make
-diff --git a/deps/xg/deps/gfakluge/Makefile b/deps/xg/deps/gfakluge/Makefile
-index b299c7e..7604db3 100644
--- a/deps/xg/deps/gfakluge/Makefile
+++ b/deps/xg/deps/gfakluge/Makefile
@@ -1,5 +1,5 @@
=====================================
debian/patches/libVCFH_unneeded deleted
=====================================
@@ -1,22 +0,0 @@
-From: "Michael R. Crusoe" <crusoe at debian.org>
-Date: Mon, 13 Jan 2020 15:40:42 +0100
-Subject: libVCFH is unneeded
-
-Forwarded: not-needed
----
- Makefile | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/Makefile b/Makefile
-index cb8a429..891c855 100644
---- a/Makefile
-+++ b/Makefile
-@@ -72,7 +72,7 @@ INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --cflags libfastahack) -I$(CWD)/$(INC_DIR)
-
- # Define libraries to link vg against.
- LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
--LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph $(shell $(PKG_CONFIG) --libs libfastahack)
-+LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph $(shell $(PKG_CONFIG) --libs libfastahack)
- # We omit Boost Program Options for now; we find it in a platform-dependent way.
- # By default it has no suffix
- BOOST_SUFFIX=""
=====================================
debian/patches/no_need_for_snappy deleted
=====================================
@@ -1,41 +0,0 @@
-From: "Michael R. Crusoe" <crusoe at debian.org>
-Date: Fri, 6 Sep 2019 14:16:07 +0900
-Subject: Due to other patches, snappy is no longer a dependency
-
-Forwarded: not-needed
----
- Makefile | 7 -------
- 1 file changed, 7 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index a5520e9..cc5c4d3 100644
---- a/Makefile
-+++ b/Makefile
-@@ -332,7 +332,6 @@ UNITTEST_EXE = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_BIN_DIR)/%,$(wild
-
- LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
- SDSL_DIR:=deps/sdsl-lite
--SNAPPY_DIR:=deps/snappy
- GCSA2_DIR:=deps/gcsa2
- GBWT_DIR:=deps/gbwt
- GBWTGRAPH_DIR=deps/gbwtgraph
-@@ -377,7 +376,6 @@ DEP_SHARED_OBJ = $(patsubst $(OBJ_DIR)/%.o,$(SHARED_OBJ_DIR)/%.o,$(DEP_OBJ))
- LIB_DEPS =
- LIB_DEPS += $(LIB_DIR)/libsdsl.a
- LIB_DEPS += $(LIB_DIR)/libssw.a
--LIB_DEPS += $(LIB_DIR)/libsnappy.a
- LIB_DEPS += $(LIB_DIR)/libgcsa2.a
- LIB_DEPS += $(LIB_DIR)/libgbwt.a
- LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
-@@ -537,11 +535,6 @@ endif
- $(LIB_DIR)/libssw.a: $(SSW_DIR)/*.c $(SSW_DIR)/*.cpp $(SSW_DIR)/*.h
- +. ./source_me.sh && cd $(SSW_DIR) && $(MAKE) $(FILTER) && ar rs $(CWD)/$(LIB_DIR)/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h $(CWD)/$(INC_DIR)
-
--# We need to hide -Xpreprocessor -fopenmp from Snappy, at least on Mac, because
--# it will drop the -Xpreprocessor and keep the -fopenmp and upset Clang.
--$(LIB_DIR)/libsnappy.a: $(SNAPPY_DIR)/*.cc $(SNAPPY_DIR)/*.h
-- +. ./source_me.sh && cd $(SNAPPY_DIR) && ./autogen.sh && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" ./configure --prefix=$(CWD) $(FILTER) && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" $(MAKE) libsnappy.la $(FILTER) && cp .libs/libsnappy.a $(CWD)/lib/ && cp snappy-c.h snappy-sinksource.h snappy-stubs-public.h snappy.h $(CWD)/include/
--
- $(INC_DIR)/gcsa/gcsa.h: $(LIB_DIR)/libgcsa2.a
-
- $(LIB_DIR)/libgcsa2.a: $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(wildcard $(GCSA2_DIR)/*.cpp) $(wildcard $(GCSA2_DIR)/include/gcsa/*.h)
=====================================
debian/patches/no_rpath
=====================================
@@ -3,17 +3,16 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: don't use rpath
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 3 ---
1 file changed, 3 deletions(-)
-diff --git a/Makefile b/Makefile
-index 141f5b1..be0555f 100644
--- a/Makefile
+++ b/Makefile
-@@ -227,9 +227,6 @@ else
- # Linux can have some old compilers so we want to work back to C++14
- CXX_STANDARD?=14
+@@ -237,9 +237,6 @@ else
+ # C++20 for spaceship operator and ranges
+ CXX_STANDARD?=20
- # Set an rpath for vg and dependency utils to find installed libraries
- LD_UTIL_RPATH_FLAGS="-Wl,-rpath,$(CWD)/$(LIB_DIR)"
=====================================
debian/patches/series
=====================================
@@ -1,29 +1,23 @@
-avoid_abs_confusion
-gcc-12
use_packaged_libdeflate
use_packaged_jemalloc
use_packaged_libbackward-cpp
use_packaged_elfutils
use_packaged_raptor2
-no_need_for_snappy
use_packaged_sparsehash
#use_packaged_ssw # vg depends on a fork of ssw for now
-use_packaged_fermi-lite
no_rpath
-no_pg
+#no_pg # patches only bundled deps/, which is not shipped
use_packaged_fastahack
#use_packaged_vw # debian package is out of date, missing array_parameters.h, and not in testing/stable
#use_packaged_sdsl # fails many tests, local copy is a newer snapshot than Debian's
-hardening_flags
+#hardening_flags # patches only bundled deps/, which is not shipped
#use_packaged_smithwaterman
static
-use_packaged_lz4
-parallize_better
+#use_packaged_lz4 # patches only bundled deps/, which is not shipped
+#parallize_better # patches only bundled deps/, which is not shipped
use_packaged_libtsl-hopscotch-map-dev
-libVCFH_unneeded
-better_clean
use_packaged_vcflib
use_packaged_htslib
simde
-crossbuild
-python3
+#crossbuild # patches only bundled deps/, which is not shipped
+#python3 # patches only bundled deps/, which is not shipped
=====================================
debian/patches/simde
=====================================
@@ -3,33 +3,28 @@ Date: Sat, 1 Feb 2020 15:13:31 +0100
Subject: Increase portability by using SIMD Everywhere library
Forwarded: https://github.com/vgteam/vg/pull/2867
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
- Makefile | 6 +-----
- deps/dozeu/dozeu.h | 2 +-
- deps/gssw/src/gssw.c | 2 +-
- deps/gssw/src/gssw.h | 2 +-
- deps/sdsl-lite/CMakeLists.txt | 13 -------------
- src/preflight.cpp | 27 ---------------------------
- src/preflight.hpp | 9 +--------
- 7 files changed, 5 insertions(+), 56 deletions(-)
+ Makefile | 6 +-----
+ src/preflight.cpp | 15 -------------
+ src/preflight.hpp | 6 +-----
+ 3 files changed, 2 insertions(+), 25 deletions(-)
-diff --git a/Makefile b/Makefile
-index 8101f38..b8fece4 100644
--- a/Makefile
+++ b/Makefile
-@@ -624,10 +624,7 @@ $(LIB_DIR)/libstructures.a: $(STRUCTURES_DIR)/src/include/structures/*.hpp $(STR
+@@ -789,10 +789,7 @@ $(LIB_DIR)/libstructures.a: $(STRUCTURES
$(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hpp
- +cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
+ cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
-$(INC_DIR)/simde/x86/sse4.1.h: $(DOZEU_DIR)/simde/*.h $(DOZEU_DIR)/simde/x86/*.h
-- +cp -r $(DOZEU_DIR)/simde $(INC_DIR)
+- cp -r $(DOZEU_DIR)/simde $(INC_DIR)
-
-$(INC_DIR)/dozeu/dozeu.h: $(DOZEU_DIR)/*.h $(INC_DIR)/simde/x86/sse4.1.h
+$(INC_DIR)/dozeu/dozeu.h: $(DOZEU_DIR)/*.h
- +mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/
+ mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/
$(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
-@@ -841,7 +838,6 @@ clean-vg:
+@@ -1037,7 +1034,6 @@ clean-vg:
clean:
$(RM) -r $(UNITTEST_BIN_DIR)
@@ -37,124 +32,38 @@ index 8101f38..b8fece4 100644
$(RM) -r $(LIB_DIR)
$(RM) -r $(UNITTEST_SUPPORT_OBJ_DIR)
$(RM) -r $(UNITTEST_OBJ_DIR)
-diff --git a/deps/dozeu/dozeu.h b/deps/dozeu/dozeu.h
-index 5d27362..9b9f01f 100644
---- a/deps/dozeu/dozeu.h
-+++ b/deps/dozeu/dozeu.h
-@@ -37,7 +37,7 @@
- #endif
-
- #define SIMDE_ENABLE_NATIVE_ALIASES
--#include "simde/x86/sse4.1.h"
-+#include <simde/x86/sse4.1.h>
-
- // Only turn on extern "C" after including code that can use C++ features.
- #ifdef __cplusplus
-diff --git a/deps/gssw/src/gssw.c b/deps/gssw/src/gssw.c
-index 9981bf6..7c494b8 100644
---- a/deps/gssw/src/gssw.c
-+++ b/deps/gssw/src/gssw.c
-@@ -30,7 +30,7 @@
- * Generalized to operate on graphs by Erik Garrison and renamed gssw.c
- */
- #define SIMDE_ENABLE_NATIVE_ALIASES
--#include "simde/x86/sse2.h"
-+#include <simde/x86/sse2.h>
- #include <stdint.h>
- #include <stdlib.h>
- #include <stdio.h>
-diff --git a/deps/gssw/src/gssw.h b/deps/gssw/src/gssw.h
-index 176af7d..bfa44ff 100644
---- a/deps/gssw/src/gssw.h
-+++ b/deps/gssw/src/gssw.h
-@@ -14,7 +14,7 @@
- #include <string.h>
- #include <stdbool.h>
- #define SIMDE_ENABLE_NATIVE_ALIASES
--#include "simde/x86/sse4.1.h"
-+#include <simde/x86/sse4.1.h>
-
- /*! @typedef structure of the query profile */
- struct gssw_profile;
-diff --git a/deps/sdsl-lite/CMakeLists.txt b/deps/sdsl-lite/CMakeLists.txt
-index 012ad23..a099805 100644
---- a/deps/sdsl-lite/CMakeLists.txt
-+++ b/deps/sdsl-lite/CMakeLists.txt
-@@ -79,19 +79,6 @@ if( MODE_TI )
- endif()
- endif()
-
--include(CheckSSE4_2)
--if( BUILTIN_POPCNT )
-- if( CMAKE_COMPILER_IS_GNUCXX )
-- append_cxx_compiler_flags("-msse4.2 -march=native" "GCC" CMAKE_CXX_OPT_FLAGS)
-- endif()
-- if( CMAKE_COMPILER_IS_GNUCXX )
-- append_cxx_compiler_flags("-msse4.2 -march=native" "CLANG" CMAKE_CXX_OPT_FLAGS)
-- endif()
-- if( CMAKE_COMPILER_IS_INTEL )
-- append_cxx_compiler_flags("-msse4.2 -march=native" "INTEL" CMAKE_CXX_FLAGS)
-- endif()
--endif()
--
- # check for demangle support to get pretty C++ class names
- include(FindCxaDemangle)
- if( HAVE_CXA_DEMANGLE )
-diff --git a/src/preflight.cpp b/src/preflight.cpp
-index fde71e4..8e02e8b 100644
--- a/src/preflight.cpp
+++ b/src/preflight.cpp
-@@ -1,38 +1,11 @@
- #include "preflight.hpp"
+@@ -30,21 +30,6 @@ void preflight_check() {
--#include <iostream>
--#include <cstdlib>
--
--#ifdef __x86_64__
--#include <cpuid.h>
--#endif
--
- namespace vg {
+ bool arch_ok = true;
- using namespace std;
-
- void preflight_check() {
-
-#ifdef __x86_64__
- // We assume we are on x86_64 on POSIX (and not Windows).
- // We use the method of dlib's dlib/simd/simd_check.h
--
+-
- // Define a place to put the cpuid info
- unsigned int cpuid_info[4];
--
+-
- // Call cpuid function 1 (which reports SSE4.2, and other stuff up to original AVX)
- __cpuid(1, cpuid_info[0], cpuid_info[1], cpuid_info[2], cpuid_info[3]);
--
+-
- // Bit 20 of result 2 is the SSE 4.2 flag.
- bool have_sse4_2 = cpuid_info[2] & (1 << 20);
--
-- if (!have_sse4_2) {
-- cerr << "error[vg::preflight_check]: The CPU does not support SSE4.2 instructions. VG cannot run here. "
-- << "Please use a system with SSE4.2 support." << endl;
-- exit(1);
-- }
+-
+- arch_ok &= have_sse4_2;
-#endif
-- // If not on x86_64, we are probably on ARM and using fake SSE anyway.
-
- }
+ // If not on x86_64, we are probably on ARM and using fake SSE anyway.
-diff --git a/src/preflight.hpp b/src/preflight.hpp
-index 7db872e..45a5f49 100644
+ if (!arch_ok) {
--- a/src/preflight.hpp
+++ b/src/preflight.hpp
-@@ -11,14 +11,7 @@
+@@ -11,12 +11,7 @@
namespace vg {
-/// Define a macro to tell things to be built for every X86_64 architecture, if possible.
--/// This *doesn't* work on Mac with GNU GCC and Apple libc++, because functions
--/// for x86-64 can't use std::endl, so we exclude that combination.
--#if defined(__x86_64__) && (!defined(__GNUC__) || !defined(_LIBCPP_VERSION) || !defined(__APPLE__))
+-#if defined(__x86_64__)
- #define VG_PREFLIGHT_EVERYWHERE __attribute__((__target__("arch=x86-64")))
-#else
- #define VG_PREFLIGHT_EVERYWHERE
=====================================
debian/patches/static
=====================================
@@ -4,24 +4,23 @@ Subject: For Debian, don't statically link to cairo, jansson, libstdc++,
libgcc
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
-diff --git a/Makefile b/Makefile
-index ce834db..e5b1b3c 100644
--- a/Makefile
+++ b/Makefile
-@@ -77,7 +77,7 @@ LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurse
+@@ -88,7 +88,7 @@ LD_CAIRO_LIB_FLAGS = $(shell PKG_CONFIG_
# By default it has no suffix
BOOST_SUFFIX=""
- # We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code.
--LD_STATIC_LIB_FLAGS := -lvgio $(CWD)/$(LIB_DIR)/libtabixpp.a $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -lbz2 -llzma
-+LD_STATIC_LIB_FLAGS := -lvgio $(CWD)/$(LIB_DIR)/libtabixpp.a $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -llzma
+ # We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code. These have both .so/.dylib and .a versions available.
+-LD_STATIC_LIB_FLAGS := -lvgio -lhts -ldeflate -lz -lbz2 -llzma
++LD_STATIC_LIB_FLAGS := -lvgio -lhts -ldeflate -lz -llzma
# Some of our static libraries depend on libraries that may not always be avilable in static form.
LD_STATIC_LIB_DEPS := -lpthread -lm
# Use pkg-config to find dependencies.
-@@ -275,7 +275,7 @@ endif
+@@ -333,7 +333,7 @@ endif
LD_LIB_FLAGS += "-lboost_program_options$(BOOST_SUFFIX)"
# These libs need to come after libdw if used, because libdw depends on them
@@ -30,12 +29,12 @@ index ce834db..e5b1b3c 100644
# Sometimes we need to filter the assembler output. The assembler can run during
# ./configure scripts, compiler calls, or $(MAKE) calls (other than $(MAKE)
-@@ -295,7 +295,7 @@ endif
- # When building statically, we need to tell the linker not to bail if it sees multiple definitions.
- # libc on e.g. our Jenkins host does not define malloc as weak, so other mallocs can't override it in a static build.
- # TODO: Why did this problem only begin to happen when libvw was added?
--STATIC_FLAGS=-static -static-libstdc++ -static-libgcc -Wl,--allow-multiple-definition
-+STATIC_FLAGS=-static -Wl,--allow-multiple-definition
+@@ -360,7 +360,7 @@ else
+ AUTOMAKE_MAKEFLAGS=
+ endif
- # These are put into libvg. Grab everything except main
- OBJ = $(filter-out $(OBJ_DIR)/main.o,$(patsubst $(SRC_DIR)/%.cpp,$(OBJ_DIR)/%.o,$(wildcard $(SRC_DIR)/*.cpp)))
+-STATIC_FLAGS=-static -static-libstdc++ -static-libgcc
++STATIC_FLAGS=-static
+
+ SRC = $(wildcard $(SRC_DIR)/*.cpp)
+ ALGORITHMS_SRC = $(wildcard $(ALGORITHMS_SRC_DIR)/*.cpp)
=====================================
debian/patches/use_packaged_elfutils
=====================================
@@ -3,35 +3,42 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian packages for elfutils
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 39 +--------------------------------------
1 file changed, 1 insertion(+), 38 deletions(-)
-diff --git a/Makefile b/Makefile
-index 96f22bd..c03808e 100644
--- a/Makefile
+++ b/Makefile
-@@ -235,7 +235,7 @@ else
+@@ -244,14 +244,8 @@ else
+ # Absolutely no help in a static build.
LD_LIB_FLAGS += -rdynamic
- # We want to link against the elfutils libraries
-- LD_LIB_FLAGS += -ldwfl -ldw -ldwelf -lelf -lebl
+- # We want to link against the elfutils libraries we build ourselves, in
+- # $(LIB_DIR), rather than the system ones. See the libelf.a rule for why the
+- # system libdw cannot be used in a static build.
+- # 0.195 split out two libraries 0.186 did not have, and both have to be here
+- # or the static link fails: libdwfl calls dwflst_* in libdwfl_stacktrace, and
+- # libdw, libelf and libdwfl all call the eu_* tsearch wrappers in libeu.
+- # -leu goes last because libeu calls back into none of them.
+- LD_LIB_FLAGS += -ldwfl -ldwfl_stacktrace -ldw -ldwelf -lelf -lebl -leu
++ # We want to link against the elfutils libraries
+ LD_LIB_FLAGS += -ldw -lelf
# We want to link against libatomic which the GNU C++ standard library needs.
# See <https://github.com/nodejs/node/issues/30093> and <https://stackoverflow.com/q/30591313>
-@@ -353,7 +353,6 @@ SSW_DIR:=deps/ssw/src
- LINLS_DIR:=deps/sublinear-Li-Stephens
- STRUCTURES_DIR:=deps/structures
- DOZEU_DIR:=deps/dozeu
+@@ -410,7 +404,6 @@ UNITTEST_SUPPORT_OBJ = $(UNITTEST_SUPPOR
+ UNITTEST_EXE = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_BIN_DIR)/%,$(UNITTEST_SRC))
+
+
-ELFUTILS_DIR:=deps/elfutils
- LIBVGIO_DIR:=deps/libvgio
- LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
- LIBBDSG_DIR:=deps/libbdsg
-@@ -399,15 +398,6 @@ LIB_DEPS += $(LIB_DIR)/libvgio.a
- LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
- LIB_DEPS += $(LIB_DIR)/libbdsg.a
- LIB_DEPS += $(LIB_DIR)/libxg.a
+ RAPTOR_DIR:=deps/raptor
+ MIMALLOC_DIR:=deps/mimalloc
+ SDSL_DIR:=deps/sdsl-lite
+@@ -479,17 +472,6 @@ LIB_DEPS += $(LIB_DIR)/libgfaz_core.a
+ LIB_DEPS += $(LIB_DIR)/libgfaz_compress.a
+ LIB_DEPS += $(LIB_DIR)/libcairo.a
+ LIB_DEPS += $(LIB_DIR)/libpixman-1.a
-ifneq ($(shell uname -s),Darwin)
- # On non-Mac (i.e. Linux), where ELF binaries are used, pull in libdw which
- # backward-cpp will use.
@@ -40,14 +47,17 @@ index 96f22bd..c03808e 100644
- LIB_DEPS += $(LIB_DIR)/libdwelf.a
- LIB_DEPS += $(LIB_DIR)/libebl.a
- LIB_DEPS += $(LIB_DIR)/libelf.a
+- LIB_DEPS += $(LIB_DIR)/libeu.a
+- LIB_DEPS += $(LIB_DIR)/libdwfl_stacktrace.a
-endif
- # Control variable for allocator
- # On the command line, you can `make jemalloc=off` if you definitely don't want jemalloc.
-@@ -749,33 +739,6 @@ $(INC_DIR)/simde/x86/sse4.1.h: $(DOZEU_DIR)/simde/*.h $(DOZEU_DIR)/simde/x86/*.h
- $(INC_DIR)/dozeu/dozeu.h: $(DOZEU_DIR)/*.h $(INC_DIR)/simde/x86/sse4.1.h
- +mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/
+ # Only depend on these files for the final linking stage.
+ # These libraries provide no headers to affect the vg build.
+@@ -915,43 +897,6 @@ $(LIB_DIR)/libstructures.a: $(STRUCTURES
+ $(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hpp
+ cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
+-# The rest of the elfutils libraries all come out of the one libelf.a rule below.
-$(LIB_DIR)/libebl.a: $(LIB_DIR)/libelf.a
-
-$(LIB_DIR)/libdw.a: $(LIB_DIR)/libelf.a
@@ -56,25 +66,34 @@ index 96f22bd..c03808e 100644
-
-$(LIB_DIR)/libdwfl.a: $(LIB_DIR)/libelf.a
-
+-$(LIB_DIR)/libeu.a: $(LIB_DIR)/libelf.a
+-
+-$(LIB_DIR)/libdwfl_stacktrace.a: $(LIB_DIR)/libelf.a
+-
-# We can't build elfutils from Git without "maintainer mode".
-# There are some release-only headers or something that it complains it can't find otherwise.
-# We also don't do a normal make and make install here because we don't want to build and install all the elfutils binaries and libasm.
-# We need to disable libdebuginfod or the static binary will try and load it at
-# runtime and pull in incompatible libs it depends on on whatever system it's
--# running on.
--$(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/libebl/*.c $(ELFUTILS_DIR)/libebl/*.h $(ELFUTILS_DIR)/libdw/*.c $(ELFUTILS_DIR)/libdw/*.h $(ELFUTILS_DIR)/libelf/*.c $(ELFUTILS_DIR)/libelf/*.h $(ELFUTILS_DIR)/src/*.c $(ELFUTILS_DIR)/src/*.h $(LIB_DIR)/cleaned_old_elfutils
-- +cd $(CWD)/$(INC_DIR)/ && rm -Rf elfutils gelf.h libelf.h dwarf.h libdwflP.h libdwfl.h libebl.h libelf.h
-- +. ./source_me.sh && cd $(ELFUTILS_DIR) && autoreconf -i -f && ./configure --enable-maintainer-mode --disable-libdebuginfod --disable-debuginfod --prefix=$(CWD) $(FILTER)
-- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libelf && $(MAKE) clean && $(MAKE) libelf.a $(FILTER)
-- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libebl && $(MAKE) clean && $(MAKE) libebl.a $(FILTER)
-- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libdwfl && $(MAKE) clean && $(MAKE) libdwfl.a $(FILTER)
-- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libdwelf && $(MAKE) clean && $(MAKE) libdwelf.a $(FILTER)
-- +. ./source_me.sh && cd $(ELFUTILS_DIR)/lib && $(MAKE) clean && $(MAKE) libeu.a $(FILTER)
-- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libcpu && $(MAKE) clean && $(MAKE) libcpu.a $(FILTER)
-- +. ./source_me.sh && cd $(ELFUTILS_DIR)/backends && $(MAKE) clean && $(MAKE) libebl_backends.a $(FILTER)
-- +. ./source_me.sh && cd $(ELFUTILS_DIR)/libdw && $(MAKE) clean && $(MAKE) libdw.a known-dwarf.h $(FILTER)
-- +cd $(ELFUTILS_DIR) && mkdir -p $(CWD)/$(INC_DIR)/elfutils && cp libdw/known-dwarf.h libdw/libdw.h libebl/libebl.h libelf/elf-knowledge.h version.h libdwfl/libdwfl.h libdwelf/libdwelf.h $(CWD)/$(INC_DIR)/elfutils && cp libelf/gelf.h libelf/libelf.h libdw/dwarf.h $(CWD)/$(INC_DIR) && cp libebl/libebl.a libdw/libdw.a libdwfl/libdwfl.a libdwelf/libdwelf.a libelf/libelf.a $(CWD)/$(LIB_DIR)/
+-# running on. Concretely: elfutils' debuginfod client dlopens libdebuginfod.so.1
+-# from a constructor, before main, and in a -static binary that drags the host's
+-# libc.so.6 in alongside the one we linked, which dies in __ctype_init. The
+-# distro libdw packages are all built with debuginfod enabled, so we cannot use
+-# them here however convenient they are.
+-$(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/libebl/*.c $(ELFUTILS_DIR)/libebl/*.h $(ELFUTILS_DIR)/libdw/*.c $(ELFUTILS_DIR)/libdw/*.h $(ELFUTILS_DIR)/libelf/*.c $(ELFUTILS_DIR)/libelf/*.h $(ELFUTILS_DIR)/src/*.c $(ELFUTILS_DIR)/src/*.h $(LIB_DIR)/cleaned_old_elfutils_v004
+- cd $(CWD)/$(INC_DIR)/ && rm -Rf elfutils gelf.h libelf.h dwarf.h libdwflP.h libdwfl.h libebl.h libelf.h
+- cd $(ELFUTILS_DIR) && autoreconf -i -f && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" ./configure --enable-maintainer-mode --disable-libdebuginfod --disable-debuginfod --prefix=$(CWD) $(FILTER)
+- cd $(ELFUTILS_DIR)/libelf && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(AUTOMAKE_MAKEFLAGS) libelf.a $(FILTER)
+- cd $(ELFUTILS_DIR)/libebl && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(AUTOMAKE_MAKEFLAGS) libebl.a $(FILTER)
+- cd $(ELFUTILS_DIR)/libdwfl && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(AUTOMAKE_MAKEFLAGS) libdwfl.a $(FILTER)
+- cd $(ELFUTILS_DIR)/libdwfl_stacktrace && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(AUTOMAKE_MAKEFLAGS) libdwfl_stacktrace.a $(FILTER)
+- cd $(ELFUTILS_DIR)/libdwelf && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(AUTOMAKE_MAKEFLAGS) libdwelf.a $(FILTER)
+- cd $(ELFUTILS_DIR)/lib && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(AUTOMAKE_MAKEFLAGS) libeu.a $(FILTER)
+- cd $(ELFUTILS_DIR)/libcpu && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(AUTOMAKE_MAKEFLAGS) libcpu.a $(FILTER)
+- cd $(ELFUTILS_DIR)/backends && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" && $(MAKE) $(AUTOMAKE_MAKEFLAGS) libebl_backends.a $(FILTER)
+- cd $(ELFUTILS_DIR)/libdw && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" && $(MAKE) $(AUTOMAKE_MAKEFLAGS) libdw.a known-dwarf.h $(FILTER)
+- cd $(ELFUTILS_DIR) && mkdir -p $(CWD)/$(INC_DIR)/elfutils && cp libdw/known-dwarf.h libdw/libdw.h libebl/libebl.h libelf/elf-knowledge.h version.h libdwfl/libdwfl.h libdwelf/libdwelf.h $(CWD)/$(INC_DIR)/elfutils && cp libelf/gelf.h libelf/libelf.h libdw/dwarf.h $(CWD)/$(INC_DIR) && cp libebl/libebl.a libdw/libdw.a libdwfl/libdwfl.a libdwelf/libdwelf.a libelf/libelf.a lib/libeu.a libdwfl_stacktrace/libdwfl_stacktrace.a $(CWD)/$(LIB_DIR)/
-
- $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
- +$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
- $(SHARED_OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
+ $(INC_DIR)/simde/x86/sse4.1.h: $(DOZEU_DIR)/simde/*.h $(DOZEU_DIR)/simde/x86/*.h
+ cp -r $(DOZEU_DIR)/simde $(INC_DIR)
+
=====================================
debian/patches/use_packaged_fastahack
=====================================
@@ -4,149 +4,29 @@ Subject: Use the Debian version of fastahack;
not working due to vg needing modifications to the upstream sourcecode
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 24 +++---------------------
test/Makefile | 5 +----
test/t/02_vg_construct.t | 2 +-
3 files changed, 5 insertions(+), 26 deletions(-)
-diff --git a/Makefile b/Makefile
-index be0555f..ce834db 100644
--- a/Makefile
+++ b/Makefile
-@@ -68,11 +68,11 @@ DEPGEN_FLAGS := -MMD -MP
+@@ -74,14 +74,14 @@ DEPGEN_FLAGS := -MMD -MP
# even though that's not *always* safe. See
# <https://stackoverflow.com/a/11532197> and
# <https://github.com/protocolbuffers/protobuf/issues/12998>
--INCLUDE_FLAGS :=-I$(CWD)/$(INC_DIR) -isystem $(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(UNITTEST_SUPPORT_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | tr ' ' '\n' | awk '!x[$$0]++' | tr '\n' ' ' | sed 's/ -I/ -isystem /g')
-+INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --cflags libfastahack) -I$(CWD)/$(INC_DIR) -isystem $(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(UNITTEST_SUPPORT_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | tr ' ' '\n' | awk '!x[$$0]++' | tr '\n' ' ' | sed 's/ -I/ -isystem /g')
+-INCLUDE_FLAGS :=-I$(CWD)/$(INC_DIR) -I$(CWD)/$(INC_DIR)/GFAz -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(UNITTEST_SUPPORT_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic -I$(CWD)/$(INC_DIR)/cairo $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) $(PKG_CONFIG_HEADER_DEPS) | tr ' ' '\n' | awk '!x[$$0]++' | tr '\n' ' ')
++INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --cflags libfastahack) -I$(CWD)/$(INC_DIR) -I$(CWD)/$(INC_DIR)/GFAz -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(UNITTEST_SUPPORT_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic -I$(CWD)/$(INC_DIR)/cairo $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) $(PKG_CONFIG_HEADER_DEPS) | tr ' ' '\n' | awk '!x[$$0]++' | tr '\n' ' ')
# Define libraries to link vg against.
+
+ # These need to come before library search paths from LDFLAGS or we won't
+ # prefer linking vg-installed dependencies over system ones.
LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
--LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph
-+LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph $(shell $(PKG_CONFIG) --libs libfastahack)
+-LD_LIB_FLAGS := -lvcflib -lwfa2 -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lstructures -lbdsg -lxg -lsdsl -lhandlegraph -lgfaz_compress -lgfaz_core -lzstd
++LD_LIB_FLAGS := -lvcflib -lwfa2 -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lstructures -lbdsg -lxg -lsdsl -lhandlegraph -lgfaz_compress -lgfaz_core -lzstd $(shell $(PKG_CONFIG) --libs libfastahack)
+ # We omit Cairo for now because its transitive dependencies can't be determined until after it's built. Set them lazily
+ LD_CAIRO_LIB_FLAGS = $(shell PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) pkg-config --libs --static cairo)
# We omit Boost Program Options for now; we find it in a platform-dependent way.
- # By default it has no suffix
- BOOST_SUFFIX=""
-@@ -334,7 +334,6 @@ GBWT_DIR:=deps/gbwt
- GBWTGRAPH_DIR=deps/gbwtgraph
- KFF_DIR=deps/kff-cpp-api
- PROGRESS_BAR_DIR:=deps/progress_bar
--FASTAHACK_DIR:=deps/fastahack
- VCFLIB_DIR:=deps/vcflib
- TABIXPP_DIR:=deps/tabixpp
- HTSLIB_DIR:=deps/htslib
-@@ -361,7 +360,6 @@ ATOMIC_QUEUE_DIR=deps/atomic_queue
- DEP_OBJ =
- DEP_OBJ += $(OBJ_DIR)/progress_bar.o
- DEP_OBJ += $(OBJ_DIR)/sha1.o
--DEP_OBJ += $(OBJ_DIR)/Fasta.o
- DEP_SHARED_OBJ = $(patsubst $(OBJ_DIR)/%.o,$(SHARED_OBJ_DIR)/%.o,$(DEP_OBJ))
-
- # These are libraries that we need to build before we link vg.
-@@ -379,7 +377,6 @@ LIB_DEPS += $(LIB_DIR)/libhts.a
- LIB_DEPS += $(LIB_DIR)/libtabixpp.a
- LIB_DEPS += $(LIB_DIR)/libvcflib.a
- LIB_DEPS += $(LIB_DIR)/libgssw.a
--LIB_DEPS += $(LIB_DIR)/libvcfh.a
- LIB_DEPS += $(LIB_DIR)/libsonlib.a
- LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
- LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
-@@ -482,7 +479,7 @@ get-deps:
- # And we have submodule deps to build
- deps: $(DEPS)
-
--test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BIN_DIR)/vcf2tsv $(FASTAHACK_DIR)/fastahack
-+test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BIN_DIR)/vcf2tsv
- . ./source_me.sh && cd test && prove -v t
- # Hide the compiler configuration from the doc tests, so that the ones that
- # build code can't pick up libraries out of the bg build itself. Definitely
-@@ -578,11 +575,6 @@ $(SHARED_OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/progress_bar.cpp $(PROGRES
- $(INC_DIR)/Fasta.h: $(FASTAHACK_DIR)/Fasta.h
- +. ./source_me.sh && cd $(FASTAHACK_DIR) && cp Fasta.h $(CWD)/$(INC_DIR)
-
--$(OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/Fasta.cpp $(INC_DIR)/Fasta.h $(FASTAHACK_DIR)/fastahack
-- +. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
--$(SHARED_OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/Fasta.cpp $(INC_DIR)/Fasta.h $(FASTAHACK_DIR)/fastahack
-- +. ./source_me.sh && $(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
--
- # We have this target to clean up the old Protobuf we used to have.
- # We can remove it after we no longer care about building properly on a dirty
- # build from vg versions that shipped Protobuf themselves.
-@@ -659,9 +651,6 @@ $(LIB_DIR)/libvcflib.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libtabixpp.a $(VCFLIB_DIR
- $(BIN_DIR)/vcf2tsv: $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.h $(LIB_DIR)/libvcflib.a
- +cp $(VCFLIB_DIR)/build/vcf2tsv $(BIN_DIR)
-
--$(FASTAHACK_DIR)/fastahack: $(FASTAHACK_DIR)/*.c $(FASTAHACK_DIR)/*.h $(FASTAHACK_DIR)/*.cpp
-- +. ./source_me.sh && cd $(FASTAHACK_DIR) && $(MAKE) $(FILTER)
--
- $(LIB_DIR)/libgssw.a: $(GSSW_DIR)/src/gssw.c $(GSSW_DIR)/src/gssw.h
- +. ./source_me.sh && cd $(GSSW_DIR) && $(MAKE) $(FILTER) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
-
-@@ -680,10 +669,6 @@ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMIC_DIR)/include/dynamic/*.hpp $(DYNAMIC_D
- $(INC_DIR)/sparsepp/spp.h:
- +cp -r $(SPARSEPP_DIR)/sparsepp $(INC_DIR)/
-
--#$(INC_DIR)/Variant.h
--$(LIB_DIR)/libvcfh.a: $(DEP_DIR)/libVCFH/*.cpp $(DEP_DIR)/libVCFH/*.hpp
-- +. ./source_me.sh && cd $(DEP_DIR)/libVCFH && $(MAKE) $(FILTER) && cp libvcfh.a $(CWD)/$(LIB_DIR)/ && cp vcfheader.hpp $(CWD)/$(INC_DIR)/
--
- $(LIB_DIR)/libsonlib.a: $(CWD)/$(DEP_DIR)/sonLib/C/inc/*.h $(CWD)/$(DEP_DIR)/sonLib/C/impl/*.c
- +. ./source_me.sh && cd $(DEP_DIR)/sonLib && kyotoTycoonLib="" $(MAKE) $(FILTER) && cp lib/sonLib.a $(CWD)/$(LIB_DIR)/libsonlib.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
-
-@@ -930,7 +915,6 @@ clean: clean-vcflib
- cd $(DEP_DIR) && cd htslib && $(MAKE) clean
- cd $(DEP_DIR) && cd tabixpp && rm -f tabix.o libtabixpp.a
- cd $(DEP_DIR) && cd sonLib && $(MAKE) clean
-- cd $(DEP_DIR) && cd fastahack && $(MAKE) clean
- cd $(DEP_DIR) && cd gcsa2 && $(MAKE) clean
- cd $(DEP_DIR) && cd gbwt && $(MAKE) clean
- cd $(DEP_DIR) && cd gbwtgraph && $(MAKE) clean
-@@ -939,7 +923,6 @@ clean: clean-vcflib
- cd $(DEP_DIR) && cd ssw && cd src && $(MAKE) clean
- cd $(DEP_DIR) && cd progress_bar && $(MAKE) clean
- cd $(DEP_DIR) && cd sdsl-lite && ./uninstall.sh || true
-- cd $(DEP_DIR) && cd libVCFH && $(MAKE) clean
- cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
- cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
- cd $(DEP_DIR) && cd structures && $(MAKE) clean
-@@ -951,5 +934,4 @@ clean: clean-vcflib
-
- clean-vcflib:
- cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
-- rm -f $(LIB_DIR)/libvcfh.a
- cd $(INC_DIR) && rm -f BedReader.h convert.h join.h mt19937ar.h split.h Variant.h vec128int.h veclib_types.h
-diff --git a/test/Makefile b/test/Makefile
-index 5ae9138..a469867 100644
---- a/test/Makefile
-+++ b/test/Makefile
-@@ -7,15 +7,12 @@ vg:=../bin/vg
-
- all: test clean
-
--test: build_graph $(vg) vcf2tsv fastahack
-+test: build_graph $(vg) vcf2tsv
- prove -v t
-
- vcf2tsv:
- cd ../deps/vcflib && $(MAKE) bin/vcf2tsv
-
--fastahack:
-- cd ../deps/fastahack && $(MAKE)
--
- $(vg):
- cd .. && $(MAKE) bin/vg
-
-diff --git a/test/t/02_vg_construct.t b/test/t/02_vg_construct.t
-index 7c9f065..d858cec 100644
---- a/test/t/02_vg_construct.t
-+++ b/test/t/02_vg_construct.t
-@@ -79,7 +79,7 @@ rm -f fail.vg
-
- # check that we produce a full graph
-
--refbp=$(../deps/fastahack/fastahack -r x small/x.fa | tr -d '\n' | wc -c)
-+refbp=$(fastahack -r x small/x.fa | tr -d '\n' | wc -c)
- variantbp=$(zcat < small/x.vcf.gz | ../bin/vcf2tsv \
- | cut -f 5,4 | tail -n+2 \
- | awk '{ x=length($2)-length($1); if (x > 0) { print x; } else if (x == 0) { print length($2); } }' \
=====================================
debian/patches/use_packaged_fermi-lite deleted
=====================================
@@ -1,45 +0,0 @@
-From: "Michael R. Crusoe" <crusoe at debian.org>
-Date: Fri, 6 Sep 2019 14:16:07 +0900
-Subject: Use the Debian package of fermi-lite
-MIME-Version: 1.0
-Content-Type: text/plain; charset="utf-8"
-Content-Transfer-Encoding: 8bit
-
-Forwarded: not-needed
-
-Adjust for the renamed bseq1_t→fml_seq1_t
-See https://github.com/lh3/fermi-lite/issues/5
----
- Makefile | 5 -----
- 1 file changed, 5 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 9761a1f..141f5b1 100644
---- a/Makefile
-+++ b/Makefile
-@@ -338,7 +338,6 @@ GBWTGRAPH_DIR=deps/gbwtgraph
- KFF_DIR=deps/kff-cpp-api
- PROGRESS_BAR_DIR:=deps/progress_bar
- FASTAHACK_DIR:=deps/fastahack
--FERMI_DIR:=deps/fermi-lite
- VCFLIB_DIR:=deps/vcflib
- TABIXPP_DIR:=deps/tabixpp
- HTSLIB_DIR:=deps/htslib
-@@ -386,7 +385,6 @@ LIB_DEPS += $(LIB_DIR)/libgssw.a
- LIB_DEPS += $(LIB_DIR)/libvcfh.a
- LIB_DEPS += $(LIB_DIR)/libsonlib.a
- LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
--LIB_DEPS += $(LIB_DIR)/libfml.a
- LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
- LIB_DEPS += $(LIB_DIR)/libstructures.a
- LIB_DEPS += $(LIB_DIR)/libvgio.a
-@@ -712,9 +710,6 @@ $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
- $(SHARED_OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
- +$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
-
--$(LIB_DIR)/libfml.a: $(FERMI_DIR)/*.h $(FERMI_DIR)/*.c
-- . ./source_me.sh && cd $(FERMI_DIR) && $(MAKE) $(FILTER) && cp *.h $(CWD)/$(INC_DIR)/ && cp libfml.a $(CWD)/$(LIB_DIR)/
--
- # We don't need to hack the build to point at our htslib because sublinearLS gets its htslib from the include flags we set
- $(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp $(LIB_DIR)/libhts.a
- . ./source_me.sh && cd $(LINLS_DIR) && $(MAKE) clean && INCLUDE_FLAGS="-I$(CWD)/$(INC_DIR)" $(MAKE) libs $(FILTER) && cp lib/libsublinearLS.a $(CWD)/$(LIB_DIR)/ && mkdir -p $(CWD)/$(INC_DIR)/sublinearLS && cp src/*.hpp $(CWD)/$(INC_DIR)/sublinearLS/
=====================================
debian/patches/use_packaged_htslib
=====================================
@@ -3,30 +3,23 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian package of htslib
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 34 ++++------------------------------
1 file changed, 4 insertions(+), 30 deletions(-)
-diff --git a/Makefile b/Makefile
-index 38f82c8..8101f38 100644
--- a/Makefile
+++ b/Makefile
-@@ -72,12 +72,12 @@ INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --cflags libfastahack) -I$(CWD)/$(INC_DIR)
-
- # Define libraries to link vg against.
+@@ -81,7 +81,7 @@ INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --
+ # These need to come before library search paths from LDFLAGS or we won't
+ # prefer linking vg-installed dependencies over system ones.
LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
--LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph $(shell $(PKG_CONFIG) --libs libfastahack)
-+LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph $(shell $(PKG_CONFIG) --libs libfastahack) $(shell $(PKG_CONFIG) --libs htslib) -ltabixpp
+-LD_LIB_FLAGS := -lvcflib -lwfa2 -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lstructures -lbdsg -lxg -lsdsl -lhandlegraph -lgfaz_compress -lgfaz_core -lzstd $(shell $(PKG_CONFIG) --libs libfastahack)
++LD_LIB_FLAGS := -lvcflib -lwfa2 -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lstructures -lbdsg -lxg -lsdsl -lhandlegraph -lgfaz_compress -lgfaz_core -lzstd $(shell $(PKG_CONFIG) --libs libfastahack) $(shell $(PKG_CONFIG) --libs htslib) -ltabixpp
+ # We omit Cairo for now because its transitive dependencies can't be determined until after it's built. Set them lazily
+ LD_CAIRO_LIB_FLAGS = $(shell PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) pkg-config --libs --static cairo)
# We omit Boost Program Options for now; we find it in a platform-dependent way.
- # By default it has no suffix
- BOOST_SUFFIX=""
- # We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code.
--LD_STATIC_LIB_FLAGS := -lvgio $(CWD)/$(LIB_DIR)/libtabixpp.a $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -llzma
-+LD_STATIC_LIB_FLAGS := -lvgio -lhts -ldeflate -lz -llzma
- # Some of our static libraries depend on libraries that may not always be avilable in static form.
- LD_STATIC_LIB_DEPS := -lpthread -lm
- # Use pkg-config to find dependencies.
-@@ -241,11 +241,6 @@ else
+@@ -251,11 +251,6 @@ else
# We get OpenMP the normal way, using whatever the compiler knows about
CXXFLAGS += -fopenmp
@@ -38,7 +31,7 @@ index 38f82c8..8101f38 100644
# Note shared libraries are so files
SHARED_SUFFIX = so
# Define options to start static linking of libraries on GNU ld.
-@@ -334,8 +329,6 @@ GBWT_DIR:=deps/gbwt
+@@ -408,8 +403,6 @@ GBWT_DIR:=deps/gbwt
GBWTGRAPH_DIR=deps/gbwtgraph
KFF_DIR=deps/kff-cpp-api
PROGRESS_BAR_DIR:=deps/progress_bar
@@ -47,7 +40,7 @@ index 38f82c8..8101f38 100644
GSSW_DIR:=deps/gssw
SPARSEPP_DIR:=deps/sparsepp
SHA1_DIR:=deps/sha1
-@@ -372,8 +365,6 @@ LIB_DEPS += $(LIB_DIR)/libgcsa2.a
+@@ -449,8 +442,6 @@ LIB_DEPS += $(LIB_DIR)/libgcsa2.a
LIB_DEPS += $(LIB_DIR)/libgbwt.a
LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
LIB_DEPS += $(LIB_DIR)/libkff.a
@@ -56,17 +49,17 @@ index 38f82c8..8101f38 100644
LIB_DEPS += $(LIB_DIR)/libgssw.a
LIB_DEPS += $(LIB_DIR)/libsonlib.a
LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
-@@ -594,7 +585,7 @@ $(LIB_DIR)/cleaned_old_elfutils:
- +rm -f $(LIB_DIR)/libelf.a $(LIB_DIR)/libebl.a $(LIB_DIR)/libdwfl.a $(LIB_DIR)/libdwelf.a $(LIB_DIR)/libdw.a
- +touch $(LIB_DIR)/cleaned_old_elfutils
+@@ -746,7 +737,7 @@ $(LIB_DIR)/cleaned_old_catch:
+ rm -f $(INC_DIR)/catch.hpp
+ touch $(LIB_DIR)/cleaned_old_catch
-$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIB_DIR)/cleaned_old_protobuf_v003 $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp $(LIBVGIO_DIR)/deps/vg.proto
+$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/cleaned_old_protobuf_v003 $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp $(LIBVGIO_DIR)/deps/vg.proto
- +rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h
- +rm -Rf $(CWD)/$(INC_DIR)/vg/io/
- +. ./source_me.sh && export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && export LDFLAGS="$(LDFLAGS) $(LD_LIB_DIR_FLAGS)" && cd $(LIBVGIO_DIR) && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_CXX_STANDARD=$(CXX_STANDARD) -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. $(FILTER) && $(MAKE) clean && VERBOSE=1 $(MAKE) $(FILTER) && $(MAKE) install
-@@ -603,21 +594,6 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLEGRAPH_DIR)/src/include/handlegraph/*.hpp
- +. ./source_me.sh && cd $(LIBHANDLEGRAPH_DIR) && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="$(CXXFLAGS) $(CPPFLAGS)" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. && $(MAKE) $(FILTER) && $(MAKE) install
+ @protoc --version >/dev/null 2>/dev/null || (echo "Error: protobuf compiler (protoc) not available!" ; exit 1)
+ rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h
+ rm -Rf $(CWD)/$(INC_DIR)/vg/io/
+@@ -762,25 +753,6 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLE
+ cd $(LIBHANDLEGRAPH_DIR)/build && $(MAKE) $(FILTER) && $(MAKE) install
-# We build htslib after libdeflate so it can use libdeflate.
@@ -79,29 +72,38 @@ index 38f82c8..8101f38 100644
-# We also need to make sure that htslib searches itself before system paths, as
-# a system path, in case another htslib is installed on the system. Some HTSlib
-# headers look for the current HTSlib with <>.
--$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
-- +. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoreconf -i && autoheader && autoconf || true
-- +. ./source_me.sh && cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
-- +. ./source_me.sh && cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
+-# Under --always-make, htslib's fallback rule for htscodecs.mk would run and
+-# write through configure's symlink into htscodecs_bundled.mk.
+-$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc $(LIB_DIR)/libhts%$(SHARED_SUFFIX): $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
+- rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts*
+- cd $(HTSLIB_DIR) && autoreconf -i && autoheader && autoconf || true
+- cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
+- cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER)
+- cd $(HTSLIB_DIR) && $(MAKE) --assume-old=htscodecs.mk clean && $(MAKE) --assume-old=htscodecs.mk $(FILTER) && $(MAKE) --assume-old=htscodecs.mk install
-
$(LIB_DIR)/libgssw.a: $(GSSW_DIR)/src/gssw.c $(GSSW_DIR)/src/gssw.h
- +. ./source_me.sh && cd $(GSSW_DIR) && $(MAKE) $(FILTER) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
-
-@@ -660,7 +636,7 @@ $(SHARED_OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
- +$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
-
+ cd $(GSSW_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER)
+ cd $(GSSW_DIR) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
+@@ -831,7 +803,7 @@ $(SHARED_OBJ_DIR)/sha1.o: $(SHA1_DIR)/sh
# We don't need to hack the build to point at our htslib because sublinearLS gets its htslib from the include flags we set
+ # But we do need to hack out the return type error to work around https://github.com/yoheirosen/sublinear-Li-Stephens/issues/6
+ # TODO: This probably means actually calling some things in the library is unsafe!
-$(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp $(LIB_DIR)/libhts.a
+$(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp
- . ./source_me.sh && cd $(LINLS_DIR) && $(MAKE) clean && INCLUDE_FLAGS="-I$(CWD)/$(INC_DIR)" $(MAKE) libs $(FILTER) && cp lib/libsublinearLS.a $(CWD)/$(LIB_DIR)/ && mkdir -p $(CWD)/$(INC_DIR)/sublinearLS && cp src/*.hpp $(CWD)/$(INC_DIR)/sublinearLS/
+ cd $(LINLS_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(filter-out -Werror=return-type,$(CFLAGS))" CXXFLAGS="-fPIC $(filter-out -Werror=return-type,$(CXXFLAGS))" INCLUDE_FLAGS="-I$(CWD)/$(INC_DIR)" $(MAKE) libs $(FILTER)
+ cd $(LINLS_DIR) && cp lib/libsublinearLS.a $(CWD)/$(LIB_DIR)/ && mkdir -p $(CWD)/$(INC_DIR)/sublinearLS && cp src/*.hpp $(CWD)/$(INC_DIR)/sublinearLS/
- $(LIB_DIR)/libbdsg.a: $(INC_DIR)/BooPHF.h $(LIBBDSG_DIR)/Makefile $(LIBBDSG_DIR)/bdsg/src/*.cpp $(LIBBDSG_DIR)/bdsg/include/bdsg/*.hpp $(LIBBDSG_DIR)/bdsg/include/bdsg/internal/*.hpp $(LIBBDSG_DIR)/bdsg/include/bdsg/overlays/*.hpp $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(INC_DIR)/sparsepp/spp.h $(INC_DIR)/dynamic/dynamic.hpp $(INC_DIR)/mio/mmap.hpp
-@@ -878,8 +854,6 @@ clean:
- $(RM) -r $(SHARED_OBJ_DIR)
- $(RM) -r $(OBJ_DIR)
- $(RM) -r share/
+@@ -1084,7 +1056,6 @@ clean:
+ cd $(DEP_DIR) && cd gbwt && $(MAKE) clean
+ cd $(DEP_DIR) && cd gbwtgraph && $(MAKE) clean
+ cd $(DEP_DIR) && cd gssw && $(MAKE) clean
- cd $(DEP_DIR) && cd htslib && $(MAKE) clean
+ cd $(DEP_DIR) && cd kff-cpp-api && rm -Rf build
+ cd $(DEP_DIR) && cd libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles
+ cd $(DEP_DIR) && cd libvgio && rm -Rf build CMakeCache.txt CMakeFiles
+@@ -1096,5 +1067,4 @@ clean:
+ cd $(DEP_DIR) && cd ssw && cd src && $(MAKE) clean
+ cd $(DEP_DIR) && cd structures && $(MAKE) clean
+ cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
- cd $(DEP_DIR) && cd tabixpp && rm -f tabix.o libtabixpp.a
- cd $(DEP_DIR) && cd sonLib && $(MAKE) clean
- cd $(DEP_DIR) && cd gcsa2 && $(MAKE) clean
- cd $(DEP_DIR) && cd gbwt && $(MAKE) clean
+
=====================================
debian/patches/use_packaged_jemalloc
=====================================
@@ -3,58 +3,67 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian packaged version of jemalloc
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 11 +++--------
1 file changed, 3 insertions(+), 8 deletions(-)
-diff --git a/Makefile b/Makefile
-index 4d65db8..252c015 100644
--- a/Makefile
+++ b/Makefile
-@@ -331,7 +331,6 @@ UNITTEST_EXE = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_BIN_DIR)/%,$(wild
-
+@@ -412,7 +412,6 @@ UNITTEST_EXE = $(patsubst $(UNITTEST_SRC
+ ELFUTILS_DIR:=deps/elfutils
RAPTOR_DIR:=deps/raptor
-JEMALLOC_DIR:=deps/jemalloc
- LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
+ MIMALLOC_DIR:=deps/mimalloc
SDSL_DIR:=deps/sdsl-lite
- SNAPPY_DIR:=deps/snappy
-@@ -424,9 +423,9 @@ LINK_DEPS =
-
- ifeq ($(jemalloc),on)
- # Use jemalloc at link time
+ GCSA2_DIR:=deps/gcsa2
+@@ -507,9 +506,9 @@ ifeq ($(mimalloc),on)
+ CONFIG_OBJ += $(CONFIG_OBJ_DIR)/allocator_config_mimalloc.o
+ else ifeq ($(jemalloc),on)
+ # Use jemalloc at link time
- LINK_DEPS += $(LIB_DIR)/libjemalloc.a
-+ LINK_DEPS += $(shell $(PKG_CONFIG) --variable=libdir jemalloc)/libjemalloc.a
- # We have to use it statically or we can't get at its secret symbols.
-- LD_LIB_FLAGS += $(LIB_DIR)/libjemalloc.a
-+ LD_LIB_FLAGS += $(shell $(PKG_CONFIG) --variable=libdir jemalloc)/libjemalloc.a
++ LINK_DEPS += $(shell $(PKG_CONFIG) --variable=libdir jemalloc)/libjemalloc.a
+ # We have to use it statically or we can't get at its secret symbols.
+- LD_EXE_LIB_FLAGS += $(LIB_DIR)/libjemalloc.a
++ LD_EXE_LIB_FLAGS += $(shell $(PKG_CONFIG) --variable=libdir jemalloc)/libjemalloc.a
# Use the config object for jemalloc
- CONFIG_OBJ += $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.o
- else
-@@ -540,9 +539,6 @@ endif
- test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/vg.hpp
- . ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp $(LDFLAGS) $(LIB_DIR)/libvg.a $(LD_LIB_DIR_FLAGS) $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(FILTER)
+ CONFIG_OBJ += $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.o
+ else ifeq ($(jemalloc),debug)
+@@ -672,19 +671,6 @@ $(LIB_DIR)/mimalloc.o: $(MIMALLOC_DIR)/s
+ cd $(MIMALLOC_DIR)/build && $(MAKE) $(FILTER)
+ cd $(MIMALLOC_DIR)/build && cp -r ../include/* $(CWD)/$(INC_DIR)/ && cp mimalloc.o $(CWD)/$(LIB_DIR)/
+-# TODO: The normal and debug jemalloc builds can't safely be run at the same time.
-$(LIB_DIR)/libjemalloc.a: $(JEMALLOC_DIR)/src/*.c
-- +. ./source_me.sh && rm -Rf $(CWD)/$(INC_DIR)/jemalloc && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --disable-libdl --prefix=`pwd` $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && cp -r lib/* $(CWD)/$(LIB_DIR)/ && cp -r include/* $(CWD)/$(INC_DIR)/
+- rm -f $(LIB_DIR)/libjemalloc*.* && rm -Rf $(CWD)/$(INC_DIR)/jemalloc
+- cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --enable-prof --disable-libdl --prefix=`pwd` $(FILTER)
+- cd $(JEMALLOC_DIR) && $(MAKE) clean && $(MAKE) $(FILTER)
+- cd $(JEMALLOC_DIR) && cp -r include/* $(CWD)/$(INC_DIR)/ && cp lib/libjemalloc.a $(CWD)/$(LIB_DIR)/
+-
+-$(LIB_DIR)/libjemalloc_debug.a: $(JEMALLOC_DIR)/src/*.c
+- rm -f $(LIB_DIR)/libjemalloc*.* && rm -Rf $(CWD)/$(INC_DIR)/jemalloc
+- cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --enable-prof --disable-libdl --enable-debug --enable-fill --prefix=`pwd` $(FILTER)
+- cd $(JEMALLOC_DIR) && $(MAKE) clean && $(MAKE) $(FILTER)
+- cd $(JEMALLOC_DIR) && cp -r include/* $(CWD)/$(INC_DIR)/ && cp lib/libjemalloc.a $(CWD)/$(LIB_DIR)/libjemalloc_debug.a
-
# Use fake patterns to tell Make that this rule generates all these files when run once.
# Here % should always match "lib" which is a common substring.
# See https://stackoverflow.com/a/19822767
-@@ -909,7 +905,7 @@ $(UNITTEST_SUPPORT_OBJ): $(UNITTEST_SUPPORT_OBJ_DIR)/%.o : $(UNITTEST_SUPPORT_SR
+@@ -1144,7 +1130,7 @@ test/build_graph.o: test/%.o : test/%.cp
+ $(CONFIG_OBJ_DIR)/allocator_config_mimalloc.o: $(CONFIG_SRC_DIR)/allocator_config_mimalloc.cpp $(CONFIG_OBJ_DIR)/allocator_config_mimalloc.d $(DEPS) $(LIB_DIR)/mimalloc.o
+ $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
-
- # Config objects get individual rules
-$(CONFIG_OBJ_DIR)/allocator_config_jemalloc.o: $(CONFIG_SRC_DIR)/allocator_config_jemalloc.cpp $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.d $(DEPS) $(LIB_DIR)/libjemalloc.a
+$(CONFIG_OBJ_DIR)/allocator_config_jemalloc.o: $(CONFIG_SRC_DIR)/allocator_config_jemalloc.cpp $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.d $(DEPS) $(shell $(PKG_CONFIG) --variable=libdir jemalloc)/libjemalloc.a
- . ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
+ $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
- $(CONFIG_OBJ_DIR)/allocator_config_system.o: $(CONFIG_SRC_DIR)/allocator_config_system.cpp $(CONFIG_OBJ_DIR)/allocator_config_system.d $(DEPS)
-@@ -1030,7 +1026,6 @@ clean: clean-vcflib
- cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
- cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
- cd $(DEP_DIR) && cd structures && $(MAKE) clean
+ $(CONFIG_OBJ_DIR)/allocator_config_jemalloc_debug.o: $(CONFIG_SRC_DIR)/allocator_config_jemalloc_debug.cpp $(CONFIG_OBJ_DIR)/allocator_config_jemalloc_debug.d $(DEPS) $(LIB_DIR)/libjemalloc_debug.a
+@@ -1239,7 +1225,6 @@ clean: clean-vcflib
+ cd $(DEP_DIR) && cd gbwtgraph && $(MAKE) clean
+ cd $(DEP_DIR) && cd gssw && $(MAKE) clean
+ cd $(DEP_DIR) && cd htslib && $(MAKE) clean
- cd $(DEP_DIR) && cd jemalloc && $(MAKE) clean || true
- cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
+ cd $(DEP_DIR) && cd kff-cpp-api && rm -Rf build
cd $(DEP_DIR) && cd libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles
cd $(DEP_DIR) && cd libvgio && rm -Rf build CMakeCache.txt CMakeFiles
=====================================
debian/patches/use_packaged_libbackward-cpp
=====================================
@@ -3,23 +3,22 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian version of cpp-backward
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 5 -----
1 file changed, 5 deletions(-)
-diff --git a/Makefile b/Makefile
-index 252c015..96f22bd 100644
--- a/Makefile
+++ b/Makefile
-@@ -352,7 +352,6 @@ DYNAMIC_DIR:=deps/DYNAMIC
+@@ -430,7 +430,6 @@ DYNAMIC_DIR:=deps/DYNAMIC
SSW_DIR:=deps/ssw/src
LINLS_DIR:=deps/sublinear-Li-Stephens
STRUCTURES_DIR:=deps/structures
-BACKWARD_CPP_DIR:=deps/backward-cpp
DOZEU_DIR:=deps/dozeu
- ELFUTILS_DIR:=deps/elfutils
LIBVGIO_DIR:=deps/libvgio
-@@ -445,7 +444,6 @@ DEPS += $(INC_DIR)/sparsehash/sparse_hash_map
+ LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
+@@ -535,7 +534,6 @@ DEPS += $(INC_DIR)/sparsehash/sparse_has
DEPS += $(INC_DIR)/sparsepp/spp.h
DEPS += $(INC_DIR)/sha1.hpp
DEPS += $(INC_DIR)/progress_bar.hpp
@@ -27,13 +26,13 @@ index 252c015..96f22bd 100644
DEPS += $(INC_DIR)/dozeu/dozeu.h
DEPS += $(INC_DIR)/mmmultimap.hpp
DEPS += $(INC_DIR)/ips4o.hpp
-@@ -745,9 +743,6 @@ $(LIB_DIR)/libstructures.a: $(STRUCTURES_DIR)/src/include/structures/*.hpp $(STR
+@@ -917,9 +915,6 @@ $(LIB_DIR)/libstructures.a: $(STRUCTURES
$(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hpp
- +cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
+ cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
-$(INC_DIR)/backward.hpp: $(BACKWARD_CPP_DIR)/backward.hpp
-- +cp $(BACKWARD_CPP_DIR)/backward.hpp $(CWD)/$(INC_DIR)/
+- cp $(BACKWARD_CPP_DIR)/backward.hpp $(CWD)/$(INC_DIR)/
-
- $(INC_DIR)/simde/x86/sse4.1.h: $(DOZEU_DIR)/simde/*.h $(DOZEU_DIR)/simde/x86/*.h
- +cp -r $(DOZEU_DIR)/simde $(INC_DIR)
+ # The rest of the elfutils libraries all come out of the one libelf.a rule below.
+ $(LIB_DIR)/libebl.a: $(LIB_DIR)/libelf.a
=====================================
debian/patches/use_packaged_libdeflate
=====================================
@@ -3,41 +3,31 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian package for libdeflate
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 21 ++-------------------
1 file changed, 2 insertions(+), 19 deletions(-)
-diff --git a/Makefile b/Makefile
-index 9dbfe97..4d65db8 100644
--- a/Makefile
+++ b/Makefile
-@@ -77,7 +77,7 @@ LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurse
- # By default it has no suffix
- BOOST_SUFFIX=""
- # We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code.
--LD_STATIC_LIB_FLAGS := -lvgio $(CWD)/$(LIB_DIR)/libtabixpp.a $(CWD)/$(LIB_DIR)/libhts.a $(CWD)/$(LIB_DIR)/libdeflate.a -lz -lbz2 -llzma
-+LD_STATIC_LIB_FLAGS := -lvgio $(CWD)/$(LIB_DIR)/libtabixpp.a $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -lbz2 -llzma
- # Some of our static libraries depend on libraries that may not always be avilable in static form.
- LD_STATIC_LIB_DEPS := -lpthread -lm
- # Use pkg-config to find dependencies.
-@@ -356,7 +356,6 @@ STRUCTURES_DIR:=deps/structures
+@@ -433,7 +433,6 @@ LINLS_DIR:=deps/sublinear-Li-Stephens
+ STRUCTURES_DIR:=deps/structures
BACKWARD_CPP_DIR:=deps/backward-cpp
DOZEU_DIR:=deps/dozeu
- ELFUTILS_DIR:=deps/elfutils
-LIBDEFLATE_DIR:=deps/libdeflate
LIBVGIO_DIR:=deps/libvgio
LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
LIBBDSG_DIR:=deps/libbdsg
-@@ -398,7 +397,6 @@ LIB_DEPS += $(LIB_DIR)/libraptor2.a
- LIB_DEPS += $(LIB_DIR)/libfml.a
+@@ -474,7 +473,6 @@ LIB_DEPS += $(LIB_DIR)/libpinchesandcact
+ LIB_DEPS += $(LIB_DIR)/libraptor2.a
LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
LIB_DEPS += $(LIB_DIR)/libstructures.a
-LIB_DEPS += $(LIB_DIR)/libdeflate.a
LIB_DEPS += $(LIB_DIR)/libvgio.a
LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
LIB_DEPS += $(LIB_DIR)/libbdsg.a
-@@ -648,21 +646,6 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLEGRAPH_DIR)/src/include/handlegraph/*.hpp
- +. ./source_me.sh && cd $(LIBHANDLEGRAPH_DIR) && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="$(CXXFLAGS) $(CPPFLAGS)" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. && $(MAKE) $(FILTER) && $(MAKE) install
+@@ -808,22 +806,6 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLE
+ cd $(LIBHANDLEGRAPH_DIR)/build && $(MAKE) $(FILTER) && $(MAKE) install
-# On Linux, libdeflate builds a .so.
@@ -45,25 +35,26 @@ index 9dbfe97..4d65db8 100644
-# On Mac we need to make sure to set the install name. We do that by renaming to dylib.
-# We don't just leave it as .so because we need to deal with outdated .so files with no paths set.
-$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX): $(LIB_DIR)/libdeflate.a
-- +cd $(LIBDEFLATE_DIR) && cp libdeflate.so $(CWD)/$(LIB_DIR)
-- +touch $(CWD)/$(LIB_DIR)/libdeflate.so
+- cd $(LIBDEFLATE_DIR) && cp libdeflate.so $(CWD)/$(LIB_DIR)
+- touch $(CWD)/$(LIB_DIR)/libdeflate.so
-ifeq ($(shell uname -s),Darwin)
-- +mv $(LIB_DIR)/libdeflate.so $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
-- +install_name_tool -id $(CWD)/$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
+- mv $(LIB_DIR)/libdeflate.so $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
+- install_name_tool -id $(CWD)/$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
-endif
-
-$(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDEFLATE_DIR)/lib/*/*.h $(LIBDEFLATE_DIR)/lib/*.c $(LIBDEFLATE_DIR)/lib/*/*.c
-- +. ./source_me.sh && cd $(LIBDEFLATE_DIR) && V=1 LDFLAGS="$(LDFLAGS) $(LD_RENAMEABLE_FLAGS)" $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
+- cd $(LIBDEFLATE_DIR) && V=1 LDFLAGS="$(LDFLAGS) $(LD_RENAMEABLE_FLAGS)" $(MAKE) $(FILTER)
+- cd $(LIBDEFLATE_DIR) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
-
# We build htslib after libdeflate so it can use libdeflate.
# We need to do some wizardry to get it to pick up the right build and target system types on modern autotools.
# We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
-@@ -673,7 +656,7 @@ $(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDE
- # We also need to make sure that htslib searches itself before system paths, as
- # a system path, in case another htslib is installed on the system. Some HTSlib
+@@ -836,7 +818,7 @@ $(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DI
# headers look for the current HTSlib with <>.
--$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(LIB_DIR)/libdeflate.a $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
-+$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
- +. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoreconf -i && autoheader && autoconf || true
- +. ./source_me.sh && cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
- +. ./source_me.sh && cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
+ # Under --always-make, htslib's fallback rule for htscodecs.mk would run and
+ # write through configure's symlink into htscodecs_bundled.mk.
+-$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc $(LIB_DIR)/libhts%$(SHARED_SUFFIX): $(LIB_DIR)/libdeflate.a $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
++$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc $(LIB_DIR)/libhts%$(SHARED_SUFFIX): $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
+ rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts*
+ cd $(HTSLIB_DIR) && autoreconf -i && autoheader && autoconf || true
+ cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
=====================================
debian/patches/use_packaged_libtsl-hopscotch-map-dev
=====================================
@@ -3,48 +3,18 @@ Date: Mon, 13 Jan 2020 13:18:24 +0100
Subject: Use the tsl-hopscotch-map cmake target
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
- Makefile | 2 +-
- deps/DYNAMIC/CMakeLists.txt | 12 +++++++++++-
- 2 files changed, 12 insertions(+), 2 deletions(-)
+ Makefile | 1 -
+ 1 file changed, 1 deletion(-)
-diff --git a/Makefile b/Makefile
-index e5b1b3c..cb8a429 100644
--- a/Makefile
+++ b/Makefile
-@@ -661,7 +661,7 @@ $(INC_DIR)/lru_cache.h: $(DEP_DIR)/lru_cache/*.h $(DEP_DIR)/lru_cache/*.cc
- $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMIC_DIR)/include/dynamic/*.hpp $(DYNAMIC_DIR)/include/dynamic/*/*.hpp
- +rm -Rf $(INC_DIR)/dynamic.hpp $(INC_DIR)/dynamic
- # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers
-- +cd $(CWD)/$(DYNAMIC_DIR) && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make && cp -r $(CWD)/$(DYNAMIC_DIR)/deps/hopscotch_map/include/* $(CWD)/$(INC_DIR)/
-+ +cd $(CWD)/$(DYNAMIC_DIR) && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && $(MAKE)
+@@ -839,7 +839,6 @@ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMI
+ rm -Rf $(CWD)/$(DYNAMIC_DIR)/build
+ cd $(CWD)/$(DYNAMIC_DIR) && mkdir -p build && cd build && export CXXFLAGS="$(CXXFLAGS)" && cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE=ON ..
+ cd $(CWD)/$(DYNAMIC_DIR)/build && export CXXFLAGS="$(CXXFLAGS)" && $(MAKE)
+- cp -r $(CWD)/$(DYNAMIC_DIR)/deps/hopscotch_map/include/* $(CWD)/$(INC_DIR)/
# Do the copy of the main file last so we can tell if this recipe failed and redo it.
# Otherwise we get dynamic.hpp without its deps
- +mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/dynamic/* $(INC_DIR)/dynamic/
-diff --git a/deps/DYNAMIC/CMakeLists.txt b/deps/DYNAMIC/CMakeLists.txt
-index 839589f..ea13ef3 100644
---- a/deps/DYNAMIC/CMakeLists.txt
-+++ b/deps/DYNAMIC/CMakeLists.txt
-@@ -19,7 +19,8 @@ include_directories(${PROJECT_SOURCE_DIR}/include)
- #include_directories(${PROJECT_SOURCE_DIR}/include/dynamic/internal)
- #include_directories(${PROJECT_SOURCE_DIR}/include/dynamic/algorithms)
- #include_directories(${PROJECT_SOURCE_DIR}/include/dynamic/algorithms/cw-bwt)
--include_directories(${CMAKE_SOURCE_DIR}/deps/hopscotch_map/include)
-+#include_directories(${CMAKE_SOURCE_DIR}/deps/hopscotch_map/include)
-+find_package(tsl-hopscotch-map REQUIRED)
-
- message("Building in ${CMAKE_BUILD_TYPE} mode")
-
-@@ -47,3 +48,12 @@ add_executable(rle_bwt rle_bwt.cpp)
- add_executable(cw-bwt cw-bwt.cpp)
- add_executable(benchmark benchmark.cpp)
- add_executable(wm_string wm_string.cpp)
-+
-+target_link_libraries(debug PRIVATE tsl::hopscotch_map)
-+target_link_libraries(rle_lz77_v1 PRIVATE tsl::hopscotch_map)
-+target_link_libraries(rle_lz77_v2 PRIVATE tsl::hopscotch_map)
-+target_link_libraries(h0_lz77 PRIVATE tsl::hopscotch_map)
-+target_link_libraries(rle_bwt PRIVATE tsl::hopscotch_map)
-+target_link_libraries(cw-bwt PRIVATE tsl::hopscotch_map)
-+target_link_libraries(benchmark PRIVATE tsl::hopscotch_map)
-+target_link_libraries(wm_string PRIVATE tsl::hopscotch_map)
+ mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/dynamic/* $(INC_DIR)/dynamic/
=====================================
debian/patches/use_packaged_raptor2
=====================================
@@ -3,31 +3,30 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian package for raptor/rapper
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 23 +----------------------
1 file changed, 1 insertion(+), 22 deletions(-)
-diff --git a/Makefile b/Makefile
-index c03808e..a5520e9 100644
--- a/Makefile
+++ b/Makefile
-@@ -330,7 +330,6 @@ UNITTEST_SUPPORT_OBJ = $(patsubst $(UNITTEST_SUPPORT_SRC_DIR)/%.cpp,$(UNITTEST_S
- UNITTEST_EXE = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_BIN_DIR)/%,$(wildcard $(UNITTEST_SRC_DIR)/*.cpp))
+@@ -404,7 +404,6 @@ UNITTEST_SUPPORT_OBJ = $(UNITTEST_SUPPOR
+ UNITTEST_EXE = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_BIN_DIR)/%,$(UNITTEST_SRC))
-RAPTOR_DIR:=deps/raptor
- LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
+ MIMALLOC_DIR:=deps/mimalloc
SDSL_DIR:=deps/sdsl-lite
- SNAPPY_DIR:=deps/snappy
-@@ -390,7 +389,6 @@ LIB_DEPS += $(LIB_DIR)/libgssw.a
- LIB_DEPS += $(LIB_DIR)/libvcfh.a
+ GCSA2_DIR:=deps/gcsa2
+@@ -461,7 +460,6 @@ LIB_DEPS += $(LIB_DIR)/libvcflib.a
+ LIB_DEPS += $(LIB_DIR)/libgssw.a
LIB_DEPS += $(LIB_DIR)/libsonlib.a
LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
-LIB_DEPS += $(LIB_DIR)/libraptor2.a
- LIB_DEPS += $(LIB_DIR)/libfml.a
LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
LIB_DEPS += $(LIB_DIR)/libstructures.a
-@@ -437,7 +435,6 @@ DEPS += $(INC_DIR)/progress_bar.hpp
+ LIB_DEPS += $(LIB_DIR)/libvgio.a
+@@ -519,7 +517,6 @@ DEPS += $(INC_DIR)/progress_bar.hpp
DEPS += $(INC_DIR)/dozeu/dozeu.h
DEPS += $(INC_DIR)/mmmultimap.hpp
DEPS += $(INC_DIR)/ips4o.hpp
@@ -35,44 +34,50 @@ index c03808e..a5520e9 100644
DEPS += $(INC_DIR)/BooPHF.h
DEPS += $(INC_DIR)/mio/mmap.hpp
DEPS += $(INC_DIR)/atomic_queue.h
-@@ -494,7 +491,7 @@ get-deps:
- # And we have submodule deps to build
- deps: $(DEPS)
+@@ -599,7 +596,7 @@ compile_commands.json: Makefile $(DEPS)
+ lint: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(ALGORITHMS_SRC_DIR)/*.cpp $(ALGORITHMS_SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp $(UNITTEST_SUPPORT_SRC_DIR)/*.cpp
+ scripts/lint.py 1>&2
--test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BIN_DIR)/vcf2tsv $(FASTAHACK_DIR)/fastahack $(BIN_DIR)/rapper
-+test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BIN_DIR)/vcf2tsv $(FASTAHACK_DIR)/fastahack
- . ./source_me.sh && cd test && prove -v t
+-test: lint $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BIN_DIR)/rapper
++test: lint $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf
+ cd test && prove -v t
# Hide the compiler configuration from the doc tests, so that the ones that
- # build code can't pick up libraries out of the bg build itself. Definitely
-@@ -710,23 +707,6 @@ $(LIB_DIR)/libsonlib.a: $(CWD)/$(DEP_DIR)/sonLib/C/inc/*.h $(CWD)/$(DEP_DIR)/son
- $(LIB_DIR)/libpinchesandcacti.a: $(LIB_DIR)/libsonlib.a $(CWD)/$(DEP_DIR)/pinchesAndCacti/inc/*.h $(CWD)/$(DEP_DIR)/pinchesAndCacti/impl/*.c
- +. ./source_me.sh && cd $(DEP_DIR)/pinchesAndCacti && $(MAKE) $(FILTER) && cd $(CWD)/$(DEP_DIR)/sonLib && cp lib/stPinchesAndCacti.a $(CWD)/$(LIB_DIR)/libpinchesandcacti.a && cp lib/3EdgeConnected.a $(CWD)/$(LIB_DIR)/lib3edgeconnected.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
+ # build code can't pick up libraries out of the vg build itself.
+@@ -867,29 +864,6 @@ $(LIB_DIR)/libpinchesandcacti.a: $(LIB_D
+ cd $(DEP_DIR)/pinchesAndCacti && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER)
+ cd $(CWD)/$(DEP_DIR)/sonLib && cp lib/stPinchesAndCacti.a $(CWD)/$(LIB_DIR)/libpinchesandcacti.a && cp lib/3EdgeConnected.a $(CWD)/$(LIB_DIR)/lib3edgeconnected.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
-# When building raptor we need to make sure to pre-generate and fix up the lexer
-# We also need to clear out its cmake stuff in case it found a wrong Bison and cached it.
-$(LIB_DIR)/libraptor2.a: $(RAPTOR_DIR)/src/* $(wildcard $(RAPTOR_DIR)/build/*)
- which bison
-- +. ./source_me.sh && cd $(RAPTOR_DIR)/build && rm -Rf CMakeCache.txt CMakeFiles CTestTestfile.cmake Makefile cmake_install.cmake src tests utils && cmake .. && rm -f src/turtle_parser.c && rm -f src/turtle_lexer.c && make turtle_lexer_tgt && make -f src/CMakeFiles/raptor2.dir/build.make src/turtle_lexer.c && sed -i.bak '/yycleanup/d' src/turtle_lexer.c && $(MAKE) $(FILTER) && cp src/libraptor2.a $(CWD)/$(LIB_DIR)
-- +touch $(LIB_DIR)/libraptor2.a
+- cd $(RAPTOR_DIR)/build && rm -Rf CMakeCache.txt CMakeFiles CTestTestfile.cmake Makefile cmake_install.cmake src tests utils
+- cd $(RAPTOR_DIR)/build && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" ..
+- cd $(RAPTOR_DIR)/build && rm -f src/turtle_parser.c && rm -f src/turtle_lexer.c
+- cd $(RAPTOR_DIR)/build && $(MAKE) turtle_lexer_tgt && $(MAKE) -f src/CMakeFiles/raptor2.dir/build.make src/turtle_lexer.c
+- cd $(RAPTOR_DIR)/build && sed -i.bak '/yycleanup/d' src/turtle_lexer.c
+- cd $(RAPTOR_DIR)/build && $(MAKE) $(FILTER)
+- cd $(RAPTOR_DIR)/build && cp src/libraptor2.a $(CWD)/$(LIB_DIR)
+- touch $(LIB_DIR)/libraptor2.a
-
-# We need rapper from Raptor for the tests
-$(BIN_DIR)/rapper: $(LIB_DIR)/libraptor2.a
-- +cp $(RAPTOR_DIR)/build/utils/rapper $(BIN_DIR)/
+- cp $(RAPTOR_DIR)/build/utils/rapper $(BIN_DIR)/
-
-# The Raptor header needs to be newer than the library.
-# Mac Travis managed to get an old header with a new binary.
-$(INC_DIR)/raptor2/raptor2.h: $(LIB_DIR)/libraptor2.a $(RAPTOR_DIR)/build/*
-- +cd $(RAPTOR_DIR)/build && mkdir -p $(CWD)/$(INC_DIR)/raptor2 && cp src/*.h $(CWD)/$(INC_DIR)/raptor2
-- +touch $(INC_DIR)/raptor2/raptor2.h
+- cd $(RAPTOR_DIR)/build && mkdir -p $(CWD)/$(INC_DIR)/raptor2 && cp src/*.h $(CWD)/$(INC_DIR)/raptor2
+- touch $(INC_DIR)/raptor2/raptor2.h
-
$(LIB_DIR)/libstructures.a: $(STRUCTURES_DIR)/src/include/structures/*.hpp $(STRUCTURES_DIR)/src/*.cpp $(STRUCTURES_DIR)/Makefile
- +. ./source_me.sh && cd $(STRUCTURES_DIR) && $(MAKE) clean && $(MAKE) lib/libstructures.a $(FILTER) && cp lib/libstructures.a $(CWD)/$(LIB_DIR)/ && cp -r src/include/structures $(CWD)/$(INC_DIR)/
-
-@@ -987,7 +967,6 @@ clean: clean-vcflib
- cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
- cd $(DEP_DIR) && cd libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles
+ cd $(STRUCTURES_DIR) && $(MAKE) clean && $(MAKE) lib/libstructures.a $(FILTER)
+ cd $(STRUCTURES_DIR) && cp lib/libstructures.a $(CWD)/$(LIB_DIR)/ && cp -r src/include/structures $(CWD)/$(INC_DIR)/
+@@ -1170,7 +1144,6 @@ clean: clean-vcflib
cd $(DEP_DIR) && cd libvgio && rm -Rf build CMakeCache.txt CMakeFiles
+ cd $(DEP_DIR) && cd mimalloc && rm -Rf build CMakeCache.txt CMakeFiles
+ cd $(DEP_DIR) && cd progress_bar && $(MAKE) clean
- cd $(DEP_DIR) && cd raptor && cd build && find . -not \( -name '.gitignore' -or -name 'pkg.m4' \) -delete
- # lru_cache is never built because it is header-only
- # bash-tap is never built either
-
+ cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
+ cd $(DEP_DIR) && cd sdsl-lite && ./uninstall.sh || true
+ cd $(DEP_DIR) && cd sonLib && $(MAKE) clean
=====================================
debian/patches/use_packaged_sparsehash
=====================================
@@ -3,15 +3,14 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian package for sparsehash
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 8 +-------
1 file changed, 1 insertion(+), 7 deletions(-)
-diff --git a/Makefile b/Makefile
-index cc5c4d3..9761a1f 100644
--- a/Makefile
+++ b/Makefile
-@@ -343,7 +343,6 @@ VCFLIB_DIR:=deps/vcflib
+@@ -415,7 +415,6 @@ VCFLIB_DIR:=deps/vcflib
TABIXPP_DIR:=deps/tabixpp
HTSLIB_DIR:=deps/htslib
GSSW_DIR:=deps/gssw
@@ -19,7 +18,7 @@ index cc5c4d3..9761a1f 100644
SPARSEPP_DIR:=deps/sparsepp
SHA1_DIR:=deps/sha1
DYNAMIC_DIR:=deps/DYNAMIC
-@@ -426,7 +425,6 @@ DEPS += $(INC_DIR)/gbwtgraph/gbwtgraph.h
+@@ -510,7 +509,6 @@ DEPS += $(INC_DIR)/gbwtgraph/gbwtgraph.h
DEPS += $(INC_DIR)/kff_io.hpp
DEPS += $(INC_DIR)/lru_cache.h
DEPS += $(INC_DIR)/dynamic/dynamic.hpp
@@ -27,23 +26,22 @@ index cc5c4d3..9761a1f 100644
DEPS += $(INC_DIR)/sparsepp/spp.h
DEPS += $(INC_DIR)/sha1.hpp
DEPS += $(INC_DIR)/progress_bar.hpp
-@@ -684,10 +682,7 @@ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMIC_DIR)/include/dynamic/*.hpp $(DYNAMIC_D
+@@ -849,10 +847,6 @@ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMI
# Otherwise we get dynamic.hpp without its deps
- +mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/dynamic/* $(INC_DIR)/dynamic/
+ mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/dynamic/* $(INC_DIR)/dynamic/
-$(INC_DIR)/sparsehash/sparse_hash_map: $(wildcard $(SPARSEHASH_DIR)/**/*.cc) $(wildcard $(SPARSEHASH_DIR)/**/*.h)
-- +. ./source_me.sh && cd $(SPARSEHASH_DIR) && ./autogen.sh && LDFLAGS="$(LDFLAGS) $(LD_LIB_DIR_FLAGS)" ./configure --prefix=$(CWD) $(FILTER) && $(MAKE) $(FILTER) && $(MAKE) install
+- cd $(SPARSEHASH_DIR) && ./autogen.sh && LDFLAGS="$(LD_LIB_DIR_FLAGS) $(LDFLAGS)" ./configure --prefix=$(CWD) $(FILTER)
+- cd $(SPARSEHASH_DIR) && $(MAKE) $(AUTOMAKE_MAKEFLAGS) src/sparsehash/internal/sparseconfig.h $(FILTER) && $(MAKE) $(AUTOMAKE_MAKEFLAGS) install-data $(FILTER)
-
--$(INC_DIR)/sparsepp/spp.h: $(wildcard $(SPARSEHASH_DIR)/sparsepp/*.h)
-+$(INC_DIR)/sparsepp/spp.h:
- +cp -r $(SPARSEPP_DIR)/sparsepp $(INC_DIR)/
+ $(INC_DIR)/sparsepp/spp.h: $(wildcard $(SPARSEPP_DIR)/sparsepp/*.h)
+ cp -r $(SPARSEPP_DIR)/sparsepp $(INC_DIR)/
- #$(INC_DIR)/Variant.h
-@@ -943,7 +938,6 @@ clean: clean-vcflib
- cd $(DEP_DIR) && cd htslib && $(MAKE) clean
- cd $(DEP_DIR) && cd tabixpp && rm -f tabix.o libtabixpp.a
+@@ -1147,7 +1141,6 @@ clean: clean-vcflib
+ cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
+ cd $(DEP_DIR) && cd sdsl-lite && ./uninstall.sh || true
cd $(DEP_DIR) && cd sonLib && $(MAKE) clean
-- cd $(DEP_DIR) && cd sparsehash && $(MAKE) clean || true
- cd $(DEP_DIR) && cd fastahack && $(MAKE) clean
- cd $(DEP_DIR) && cd gcsa2 && $(MAKE) clean
- cd $(DEP_DIR) && cd gbwt && $(MAKE) clean
+- cd $(DEP_DIR) && cd sparsehash && $(MAKE) $(AUTOMAKE_MAKEFLAGS) clean || true
+ cd $(DEP_DIR) && cd ssw && cd src && $(MAKE) clean
+ cd $(DEP_DIR) && cd structures && $(MAKE) clean
+ cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
=====================================
debian/patches/use_packaged_vcflib
=====================================
@@ -3,6 +3,7 @@ Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Attempt to use the Debian version of vcflib
Forwarded: not-needed
+Assisted-By: scaleway/deepseek-v4-flash-0731
---
Makefile | 39 +--------------------------------------
src/aligner.hpp | 2 +-
@@ -18,11 +19,9 @@ Forwarded: not-needed
test/t/02_vg_construct.t | 2 +-
12 files changed, 12 insertions(+), 57 deletions(-)
-diff --git a/Makefile b/Makefile
-index 848d221..38f82c8 100644
--- a/Makefile
+++ b/Makefile
-@@ -334,7 +334,6 @@ GBWT_DIR:=deps/gbwt
+@@ -408,7 +408,6 @@ GBWT_DIR:=deps/gbwt
GBWTGRAPH_DIR=deps/gbwtgraph
KFF_DIR=deps/kff-cpp-api
PROGRESS_BAR_DIR:=deps/progress_bar
@@ -30,7 +29,7 @@ index 848d221..38f82c8 100644
TABIXPP_DIR:=deps/tabixpp
HTSLIB_DIR:=deps/htslib
GSSW_DIR:=deps/gssw
-@@ -375,7 +374,6 @@ LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
+@@ -452,7 +451,6 @@ LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
LIB_DEPS += $(LIB_DIR)/libkff.a
LIB_DEPS += $(LIB_DIR)/libhts.a
LIB_DEPS += $(LIB_DIR)/libtabixpp.a
@@ -38,73 +37,76 @@ index 848d221..38f82c8 100644
LIB_DEPS += $(LIB_DIR)/libgssw.a
LIB_DEPS += $(LIB_DIR)/libsonlib.a
LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
-@@ -620,37 +618,6 @@ $(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(HTSLIB_DIR)/*.c $(HTSLIB_D
- +. ./source_me.sh && cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
- +. ./source_me.sh && cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
+@@ -783,48 +781,6 @@ $(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig
+ cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER)
+ cd $(HTSLIB_DIR) && $(MAKE) --assume-old=htscodecs.mk clean && $(MAKE) --assume-old=htscodecs.mk $(FILTER) && $(MAKE) --assume-old=htscodecs.mk install
-# Build and install tabixpp for vcflib.
-$(LIB_DIR)/libtabixpp.a: $(LIB_DIR)/libhts.a $(TABIXPP_DIR)/*.cpp $(TABIXPP_DIR)/*.hpp
-- +. ./source_me.sh && cd $(TABIXPP_DIR) && rm -f tabix.o libtabixpp.a && INCLUDES="-I$(CWD)/$(INC_DIR)" HTS_HEADERS="" $(MAKE) tabix.o $(FILTER) && ar rcs libtabixpp.a tabix.o
-- +cp $(TABIXPP_DIR)/libtabixpp.a $(LIB_DIR) && cp $(TABIXPP_DIR)/tabix.hpp $(INC_DIR)
-- +echo "Name: tabixpp" > $(LIB_DIR)/pkgconfig/tabixpp.pc
-- +echo "Description: Self-packaged tabixpp" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
-- +echo "Version: 1.0" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
-- +echo "Cflags: -I$(CWD)/$(INC_DIR)" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
-- +echo "Libs: -L$(CWD)/$(LIB_DIR) -ltabixpp" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
+- cd $(TABIXPP_DIR) && rm -f tabix.o libtabixpp.a
+- cd $(TABIXPP_DIR) && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" INCLUDES="$(INCLUDE_FLAGS)" HTS_HEADERS="" $(MAKE) tabix.o $(FILTER)
+- cd $(TABIXPP_DIR) && ar rcs libtabixpp.a tabix.o
+- cp $(TABIXPP_DIR)/libtabixpp.a $(LIB_DIR) && cp $(TABIXPP_DIR)/tabix.hpp $(INC_DIR)
+- echo "Name: tabixpp" > $(LIB_DIR)/pkgconfig/tabixpp.pc
+- echo "Description: Self-packaged tabixpp" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
+- echo "Version: 1.0" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
+- echo "Cflags: -I$(CWD)/$(INC_DIR)" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
+- echo "Libs: -L$(CWD)/$(LIB_DIR) -ltabixpp" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
-
--# Build vcflib. Install the library and headers but not binaries or man pages.
--# We need to build as RelWithDebInfo to avoid vcflib using its own
+-# Build vcflib. Build the library and any needed binaries. Install the library
+-# and headers but not binaries or man pages. We need to build as RelWithDebInfo
+-# to avoid vcflib using its own
-# -march=native, which would conflict with the -march that comes in through
--# CXXFLAGS from the vg Dockerfile.
--# We also need to use the magic path hint to let CMake find Mac OpenMP.
--# We need to use /usr first for CMake search or Ubuntu 22.04 will decide pybind11 is installed in / when actually it is only fully installed in /usr.
--$(LIB_DIR)/libvcflib.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libtabixpp.a $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.hpp $(VCFLIB_DIR)/contrib/*/*.cpp $(VCFLIB_DIR)/contrib/*/*.h
-- +rm -f $(VCFLIB_DIR)/contrib/WFA2-lib/VERSION
-- +. ./source_me.sh && cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS) ${CPPFLAGS}" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" .. && cmake --build .
-- +cp $(VCFLIB_DIR)/contrib/filevercmp/*.h* $(INC_DIR)
-- +cp $(VCFLIB_DIR)/contrib/fastahack/*.h* $(INC_DIR)
-- +cp $(VCFLIB_DIR)/contrib/smithwaterman/*.h* $(INC_DIR)
-- +cp $(VCFLIB_DIR)/contrib/intervaltree/*.h* $(INC_DIR)
-- +cp $(VCFLIB_DIR)/contrib/multichoose/*.h* $(INC_DIR)
-- +cp $(VCFLIB_DIR)/src/*.h* $(INC_DIR)
-- +cp $(VCFLIB_DIR)/build/libvcflib.a $(LIB_DIR)
--
--# vcflib binaries are all automatically built. We need this one.
--$(BIN_DIR)/vcf2tsv: $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.h $(LIB_DIR)/libvcflib.a
-- +cp $(VCFLIB_DIR)/build/vcf2tsv $(BIN_DIR)
+-# CXXFLAGS from the vg Dockerfile. We also need to use the magic path hint to
+-# let CMake find Mac OpenMP. We need to use /usr first for CMake search or
+-# Ubuntu 22.04 will decide pybind11 is installed in / when actually it is only
+-# fully installed in /usr.
+-# We also have to make sure to point at a Python that probably has its headers,
+-# because there's no way to turn off vcflib's pybind11 build and pybind11 will
+-# try and use the latest installed Python over the default one that probably
+-# has headers.
+-# We now need to tell it to build in static mode so we get a static library.
+-# And we also now need to tell it to actually build its bundled WFA.
+-#
+-# Note that on MacOS we rely on the Makefile putting GNU coreutils on the PATH
+-# in order to avoid the dreaded "Could NOT find Threads".
+-$(LIB_DIR)/libvcflib%a $(LIB_DIR)/libwfa2%a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libtabixpp.a $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.hpp $(VCFLIB_DIR)/contrib/*/*.cpp $(VCFLIB_DIR)/contrib/*/*.h $(LIB_DIR)/cleaned_old_catch
+- rm -f $(VCFLIB_DIR)/contrib/WFA2-lib/VERSION
+- env
+- cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS)" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" -DPYTHON_EXECUTABLE="$(shell which python3)" -DBUILD_STATIC=ON -DWFA_GITMODULE=ON .. && cmake --build . --target vcflib wfa2_static
+- cp $(VCFLIB_DIR)/contrib/filevercmp/*.h* $(INC_DIR)
+- cp $(VCFLIB_DIR)/contrib/fastahack/*.h* $(INC_DIR)
+- cp $(VCFLIB_DIR)/contrib/smithwaterman/*.h* $(INC_DIR)
+- cp $(VCFLIB_DIR)/contrib/intervaltree/IntervalTree.h $(INC_DIR)
+- cp $(VCFLIB_DIR)/contrib/multichoose/*.h* $(INC_DIR)
+- cp $(VCFLIB_DIR)/src/*.h* $(INC_DIR)
+- cp $(VCFLIB_DIR)/build/libvcflib.a $(LIB_DIR)
+- cp $(VCFLIB_DIR)/build/contrib/WFA2-lib/libwfa2.a $(LIB_DIR)
-
$(LIB_DIR)/libgssw.a: $(GSSW_DIR)/src/gssw.c $(GSSW_DIR)/src/gssw.h
- +. ./source_me.sh && cd $(GSSW_DIR) && $(MAKE) $(FILTER) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
-
-@@ -896,7 +863,7 @@ clean-vg:
+ cd $(GSSW_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER)
+ cd $(GSSW_DIR) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
+@@ -1107,7 +1063,7 @@ clean-vg:
$(RM) -f $(IO_SHARED_OBJ_DIR)/*.o $(IO_SHARED_OBJ_DIR)/*.d
- $(RM) -f $(INC_DIR)/vg_git_version.hpp
+ $(RM) -f $(SRC_DIR)/vg_git_version.hpp $(SRC_DIR)/vg_environment_version.hpp
-clean: clean-vcflib
+clean:
$(RM) -r $(UNITTEST_BIN_DIR)
$(RM) -r $(BIN_DIR)
$(RM) -r $(LIB_DIR)
-@@ -922,7 +889,6 @@ clean: clean-vcflib
- cd $(DEP_DIR) && cd ssw && cd src && $(MAKE) clean
- cd $(DEP_DIR) && cd progress_bar && $(MAKE) clean
- cd $(DEP_DIR) && cd sdsl-lite && ./uninstall.sh || true
-- cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
- cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
+@@ -1141,8 +1097,4 @@ clean: clean-vcflib
cd $(DEP_DIR) && cd structures && $(MAKE) clean
cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
-@@ -931,6 +897,3 @@ clean: clean-vcflib
- # lru_cache is never built because it is header-only
- # bash-tap is never built either
+ cd $(DEP_DIR) && cd tabixpp && rm -f tabix.o libtabixpp.a
+- cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
-clean-vcflib:
- cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
- cd $(INC_DIR) && rm -f BedReader.h convert.h join.h mt19937ar.h split.h Variant.h vec128int.h veclib_types.h
-diff --git a/src/aligner.hpp b/src/aligner.hpp
-index 04a080f..d1a396f 100644
--- a/src/aligner.hpp
+++ b/src/aligner.hpp
-@@ -11,7 +11,7 @@
+@@ -12,7 +12,7 @@
#include <vg/vg.pb.h>
#include "gssw.h"
@@ -113,8 +115,6 @@ index 04a080f..d1a396f 100644
#include "Fasta.h"
#include "handle.hpp"
#include "path.hpp"
-diff --git a/src/clip.cpp b/src/clip.cpp
-index 4b0934f..d023dce 100644
--- a/src/clip.cpp
+++ b/src/clip.cpp
@@ -1,7 +1,7 @@
@@ -126,8 +126,6 @@ index 4b0934f..d023dce 100644
#include <structures/rank_pairing_heap.hpp>
#include <BooPHF.h>
#include "bdsg/internal/hash_map.hpp"
-diff --git a/src/constructor.cpp b/src/constructor.cpp
-index 127a9a3..30d8880 100644
--- a/src/constructor.cpp
+++ b/src/constructor.cpp
@@ -8,7 +8,7 @@
@@ -139,8 +137,6 @@ index 127a9a3..30d8880 100644
#include <cstdlib>
#include <set>
-diff --git a/src/constructor.hpp b/src/constructor.hpp
-index 9b682a4..4089b68 100644
--- a/src/constructor.hpp
+++ b/src/constructor.hpp
@@ -22,7 +22,7 @@
@@ -152,21 +148,17 @@ index 9b682a4..4089b68 100644
// And fastahack
#include <Fasta.h>
-diff --git a/src/deconstructor.hpp b/src/deconstructor.hpp
-index ee53749..0cfb442 100644
--- a/src/deconstructor.hpp
+++ b/src/deconstructor.hpp
-@@ -7,7 +7,7 @@
- #include <algorithm>
+@@ -8,7 +8,7 @@
#include <atomic>
+ #include <memory>
#include "genotypekit.hpp"
-#include "Variant.h"
+#include <vcflib/Variant.h>
#include "handle.hpp"
#include "traversal_finder.hpp"
#include "graph_caller.hpp"
-diff --git a/src/readfilter.hpp b/src/readfilter.hpp
-index 0716721..acb47a4 100644
--- a/src/readfilter.hpp
+++ b/src/readfilter.hpp
@@ -11,7 +11,7 @@
@@ -177,9 +169,7 @@ index 0716721..acb47a4 100644
+#include <intervaltree/IntervalTree.h>
#include "annotation.hpp"
#include "multipath_alignment_emitter.hpp"
- #include <vg/io/alignment_emitter.hpp>
-diff --git a/src/utility.hpp b/src/utility.hpp
-index 434b026..6c681af 100644
+ #include "progressive.hpp"
--- a/src/utility.hpp
+++ b/src/utility.hpp
@@ -19,7 +19,7 @@
@@ -188,11 +178,9 @@ index 434b026..6c681af 100644
#include "sha1.hpp"
-#include "Variant.h"
+#include <vcflib/Variant.h>
+ #include "log.hpp"
namespace vg {
-
-diff --git a/src/vcf_buffer.hpp b/src/vcf_buffer.hpp
-index 0dc61e4..1cdeb53 100644
--- a/src/vcf_buffer.hpp
+++ b/src/vcf_buffer.hpp
@@ -10,7 +10,7 @@
@@ -204,8 +192,6 @@ index 0dc61e4..1cdeb53 100644
namespace vg {
-diff --git a/src/vg.hpp b/src/vg.hpp
-index 3e8652f..1a1ba9b 100644
--- a/src/vg.hpp
+++ b/src/vg.hpp
@@ -33,7 +33,7 @@
@@ -217,41 +203,3 @@ index 3e8652f..1a1ba9b 100644
#include "Fasta.h"
#include "swap_remove.hpp"
-diff --git a/test/Makefile b/test/Makefile
-index a469867..3e3e305 100644
---- a/test/Makefile
-+++ b/test/Makefile
-@@ -3,19 +3,11 @@
- CXX:=g++
- CXXFLAGS:=-O3 -std=c++11 -fopenmp -g
-
--vg:=../bin/vg
--
- all: test clean
-
--test: build_graph $(vg) vcf2tsv
-+test: build_graph
- prove -v t
-
--vcf2tsv:
-- cd ../deps/vcflib && $(MAKE) bin/vcf2tsv
--
--$(vg):
-- cd .. && $(MAKE) bin/vg
--
- build_graph: build_graph.cpp
- cd .. && . ./source_me.sh && $(MAKE) test/build_graph
-
-diff --git a/test/t/02_vg_construct.t b/test/t/02_vg_construct.t
-index d858cec..90a9fa7 100644
---- a/test/t/02_vg_construct.t
-+++ b/test/t/02_vg_construct.t
-@@ -80,7 +80,7 @@ rm -f fail.vg
- # check that we produce a full graph
-
- refbp=$(fastahack -r x small/x.fa | tr -d '\n' | wc -c)
--variantbp=$(zcat < small/x.vcf.gz | ../bin/vcf2tsv \
-+variantbp=$(zcat < small/x.vcf.gz | vcf2tsv \
- | cut -f 5,4 | tail -n+2 \
- | awk '{ x=length($2)-length($1); if (x > 0) { print x; } else if (x == 0) { print length($2); } }' \
- | awk '{ sum += $1 } END { print sum }')
View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/f9dea267377625165bf1564598f31de07f2db35e...9b5c9d6b9a5fb7ae71a46082dd23202fe6100b92
--
View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/f9dea267377625165bf1564598f31de07f2db35e...9b5c9d6b9a5fb7ae71a46082dd23202fe6100b92
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