[med-svn] [Git][med-team/vg][master] 12 commits: New upstream version 1.20.0+ds
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Jan 13 14:29:21 GMT 2020
Michael R. Crusoe pushed to branch master at Debian Med / vg
Commits:
16471a93 by Michael R. Crusoe at 2019-12-09T17:24:58+01:00
New upstream version 1.20.0+ds
- - - - -
fdadbc62 by Michael R. Crusoe at 2019-12-09T17:26:53+01:00
Update upstream source from tag 'upstream/1.20.0+ds'
Update to upstream version '1.20.0+ds'
with Debian dir 2ffb323d6c5b9474305597579882f85098a298db
- - - - -
44bff222 by Michael R. Crusoe at 2019-12-09T17:27:13+01:00
update changelog for docker pull 1.20.0+ds-1
- - - - -
56971a7f by Michael R. Crusoe at 2019-12-09T17:49:59+01:00
refresh patches
- - - - -
3f3dd896 by Michael R. Crusoe at 2020-01-13T11:32:02+01:00
routine-update: New upstream version
- - - - -
8a1a8261 by Michael R. Crusoe at 2020-01-13T11:36:44+01:00
New upstream version 1.21.0+ds
- - - - -
901ddc96 by Michael R. Crusoe at 2020-01-13T11:38:29+01:00
Update upstream source from tag 'upstream/1.21.0+ds'
Update to upstream version '1.21.0+ds'
with Debian dir 7fcf5965073a3eda7c5b9045fb11ff8974d89884
- - - - -
df0cc656 by Michael R. Crusoe at 2020-01-13T12:08:49+01:00
freshen patches
- - - - -
2d7a0c99 by Michael R. Crusoe at 2020-01-13T13:35:45+01:00
libtsl-hopscotch-map-dev is now available!
- - - - -
57d012c5 by Michael R. Crusoe at 2020-01-13T13:55:51+01:00
Merge remote-tracking branch 'origin/master'
- - - - -
0c20a605 by Michael R. Crusoe at 2020-01-13T14:08:44+01:00
remove errant libdeflate.a
- - - - -
fa250714 by Michael R. Crusoe at 2020-01-13T14:09:58+01:00
don't forget about use_packaged_protobuf
- - - - -
24 changed files:
- debian/changelog
- debian/control
- debian/patches/hardening_flags
- debian/patches/no_need_for_snappy
- debian/patches/no_pg
- debian/patches/no_rpath
- debian/patches/parallize_better
- debian/patches/series
- debian/patches/spelling
- debian/patches/static
- debian/patches/use_packaged_boost
- debian/patches/use_packaged_elfutils
- debian/patches/use_packaged_fastahack
- debian/patches/use_packaged_fermi-lite
- 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_protobuf
- debian/patches/use_packaged_raptor2
- debian/patches/use_packaged_rocksdb
- debian/patches/use_packaged_smithwaterman
- debian/patches/use_packaged_sparsehash
- debian/patches/use_packaged_ssw
Changes:
=====================================
debian/changelog
=====================================
@@ -2,4 +2,4 @@ vg (1.21.0+ds-1) UNRELEASED; urgency=medium
* Initial release. (Closes: #939537)
- -- Michael R. Crusoe <michael.crusoe at gmail.com> Sun, 12 Jan 2020 08:30:00 +0100
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 13 Jan 2020 11:32:02 +0100
=====================================
debian/control
=====================================
@@ -55,7 +55,8 @@ Build-Depends: debhelper-compat (= 12),
fastahack,
libsmithwaterman-dev,
libjs-d3,
- libdivsufsort-dev
+ libdivsufsort-dev,
+ libtsl-hopscotch-map-dev
# libvcflib-dev (>= 1.0),
# libhts-dev
# libsdsl-dev,
=====================================
debian/patches/hardening_flags
=====================================
@@ -2,8 +2,8 @@ From: Michael R. Crusoe <michael.crusoe at gmail.com>
Subject: Make build system more flexible
So that Debian can pass hardening flags
---- a/deps/gssw/Makefile
-+++ b/deps/gssw/Makefile
+--- vg.orig/deps/gssw/Makefile
++++ vg/deps/gssw/Makefile
@@ -1,5 +1,5 @@
CC:=gcc
-CFLAGS:=-Wall -O3 -msse4 -g
@@ -11,7 +11,7 @@ So that Debian can pass hardening flags
OBJ_DIR:=obj
BIN_DIR:=bin
SRC_DIR:=src
-@@ -17,19 +17,19 @@ all:$(BIN_DIR)/$(EXE) $(BIN_DIR)/$(EXEAD
+@@ -17,19 +17,19 @@
$(BIN_DIR)/$(EXE):$(OBJ_DIR)/$(OBJ) $(SRC_DIR)/example.c
# Make dest directory
@mkdir -p $(@D)
@@ -35,9 +35,9 @@ So that Debian can pass hardening flags
$(LIB_DIR)/libgssw.a:$(OBJ_DIR)/$(OBJ)
@mkdir -p $(@D)
---- a/deps/sdsl-lite/install.sh
-+++ b/deps/sdsl-lite/install.sh
-@@ -53,7 +53,7 @@ if [ $? != 0 ]; then
+--- vg.orig/deps/sdsl-lite/install.sh
++++ vg/deps/sdsl-lite/install.sh
+@@ -53,7 +53,7 @@
exit 1
fi
@@ -46,7 +46,7 @@ So that Debian can pass hardening flags
if [ $? != 0 ]; then
echo "ERROR: CMake build failed."
exit 1
-@@ -92,10 +92,6 @@ echo "The sdsl include files are located
+@@ -92,10 +92,6 @@
echo "The library files are located in '${SDSL_INSTALL_PREFIX}/lib'."
echo " "
echo "Sample programs can be found in the examples-directory."
@@ -57,24 +57,24 @@ So that Debian can pass hardening flags
echo " "
echo "Tests in the test-directory"
echo "A cheat sheet in the extras/cheatsheet-directory."
---- a/Makefile
-+++ b/Makefile
-@@ -286,12 +286,12 @@ endif
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -286,12 +286,12 @@
# For a normal dynamic build we remove the static build marker
$(BIN_DIR)/$(EXE): $(OBJ_DIR)/main.o $(LIB_DIR)/libvg.a $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) $(DEPS) $(LINK_DEPS)
-rm -f $(LIB_DIR)/vg_is_static
- . ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(LD_LIB_FLAGS)
-+ . ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(LD_LIB_FLAGS) $(LDFLAGS)
++ . ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(LD_LIB_FLAGS)
# We keep a file that we touch on the last static build.
# If the vg linkables are newer than the last static build, we do a build
$(LIB_DIR)/vg_is_static: $(INC_DIR)/vg_environment_version.hpp $(OBJ_DIR)/main.o $(LIB_DIR)/libvg.a $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) $(DEPS) $(LINK_DEPS)
- $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(STATIC_FLAGS) $(LD_LIB_FLAGS)
-+ $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(STATIC_FLAGS) $(LD_LIB_FLAGS) $(LDFLAGS)
++ $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(STATIC_FLAGS) $(LD_LIB_FLAGS)
-touch $(LIB_DIR)/vg_is_static
# We don't want to always rebuild the static vg if no files have changed.
-@@ -338,16 +338,16 @@ else
+@@ -338,16 +338,16 @@
endif
test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/json2pb.h $(SRC_DIR)/vg.hpp
@@ -94,7 +94,7 @@ So that Debian can pass hardening flags
endif
$(INC_DIR)/gcsa/gcsa.h: $(LIB_DIR)/libgcsa2.a
-@@ -398,10 +398,10 @@ $(LIB_DIR)/cleaned_old_protobuf_v003: $(
+@@ -398,10 +398,10 @@
$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.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
+rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h
+rm -Rf $(CWD)/$(INC_DIR)/vg/io/
@@ -106,18 +106,18 @@ So that Debian can pass hardening flags
+ +. ./source_me.sh && cd $(LIBHANDLEGRAPH_DIR) && CXXFLAGS="$(CXXFLAGS) $(CPPFLAGS)" cmake . && $(MAKE) $(FILTER) && cp libhandlegraph.a $(CWD)/$(LIB_DIR) && cp -r src/include/handlegraph $(CWD)/$(INC_DIR)
- # We also have to have the shared libdeflate or we will get complaints that the static one is not position independent.
-@@ -409,7 +409,7 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLE
+ # We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
+@@ -410,7 +410,7 @@
# We use a wildcard match to make sure make understands that both files come from one command run.
# See https://stackoverflow.com/a/3077254
$(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* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(INC_DIR)" LDFLAGS="-L$(CWD)/$(LIB_DIR)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
-+ +. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="-L$(CWD)/$(LIB_DIR) $(LDFLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
++ +. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="-L$(CWD)/$(LIB_DIR)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
# We tell the vcflib build to use our own htslib.
# We link it and libdeflate statically (on Linux) because our lib directory won't
-@@ -497,7 +497,7 @@ $(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/lib
- +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)/
+@@ -481,7 +481,7 @@
+ +mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/
$(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
- +$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -c -o $@ $< $(FILTER)
@@ -125,7 +125,7 @@ So that Debian can pass hardening flags
# 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
-@@ -579,19 +579,19 @@ $(OBJ_DIR)/version.o: $(SRC_DIR)/version
+@@ -563,19 +563,19 @@
# Use static pattern rules so the dependency files will not be ignored if the output exists
# See <https://stackoverflow.com/a/34983297>
$(OBJ) $(CONFIGURATION_OBJ) $(OBJ_DIR)/main.o: $(OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp $(OBJ_DIR)/%.d $(DEPS)
@@ -150,9 +150,9 @@ So that Debian can pass hardening flags
@touch $@
# Use a fake rule to build .d files, so we don't complain if they don't exist.
---- a/deps/sha1/Makefile
-+++ b/deps/sha1/Makefile
-@@ -5,10 +5,10 @@ RM = rm -f
+--- vg.orig/deps/sha1/Makefile
++++ vg/deps/sha1/Makefile
+@@ -5,10 +5,10 @@
all: demo_sha1 test_sha1
demo_sha1: demo_sha1.cpp sha1.cpp sha1.hpp
@@ -165,9 +165,9 @@ So that Debian can pass hardening flags
check: test_sha1
./test_sha1
---- a/deps/sonLib/externalTools/cutest/Makefile
-+++ b/deps/sonLib/externalTools/cutest/Makefile
-@@ -10,7 +10,7 @@ clean :
+--- vg.orig/deps/sonLib/externalTools/cutest/Makefile
++++ vg/deps/sonLib/externalTools/cutest/Makefile
+@@ -10,7 +10,7 @@
${libPath}/cuTest.a : CuTest.c CuTest.h
@mkdir -p $(dir $@)
@@ -176,9 +176,9 @@ So that Debian can pass hardening flags
ar rc cuTest.a *.o
ranlib cuTest.a
rm -f *.o
---- a/deps/sonLib/externalTools/quicktree_1.1/Makefile
-+++ b/deps/sonLib/externalTools/quicktree_1.1/Makefile
-@@ -13,43 +13,43 @@ COMMON = $(OBJ)/align.o \
+--- vg.orig/deps/sonLib/externalTools/quicktree_1.1/Makefile
++++ vg/deps/sonLib/externalTools/quicktree_1.1/Makefile
+@@ -13,43 +13,43 @@
QUICKTREEOBJ = $(COMMON) $(OBJ)/quicktree.o $(OBJ)/buildtree.o $(OBJ)/tree.o
@@ -234,9 +234,9 @@ So that Debian can pass hardening flags
clean:
rm -rf $(OBJ)/*.o
---- a/deps/structures/Makefile
-+++ b/deps/structures/Makefile
-@@ -9,7 +9,7 @@ LIB = $(LIBDIR)/libstructures.a
+--- vg.orig/deps/structures/Makefile
++++ vg/deps/structures/Makefile
+@@ -9,7 +9,7 @@
TESTOBJ =$(OBJDIR)/tests.o
HEADERS = $(INCDIR)/suffix_tree.hpp $(INCDIR)/union_find.hpp $(INCDIR)/min_max_heap.hpp $(INCDIR)/immutable_list.hpp $(INCDIR)/stable_double.hpp $(INCDIR)/rank_pairing_heap.hpp
CXX = g++
@@ -245,7 +245,7 @@ So that Debian can pass hardening flags
all:
-@@ -23,13 +23,13 @@ $(BINDIR)/test: $(TESTOBJ) $(HEADERS) $(
+@@ -23,13 +23,13 @@
$(CXX) $(CPPFLAGS) -o $(BINDIR)/test $(TESTOBJ) $(LIB)
$(OBJDIR)/suffix_tree.o: $(SRCDIR)/suffix_tree.cpp $(INCDIR)/suffix_tree.hpp
@@ -262,16 +262,16 @@ So that Debian can pass hardening flags
# MinMaxHeap is header-only
---- a/deps/gfakluge/Makefile
-+++ b/deps/gfakluge/Makefile
+--- vg.orig/deps/gfakluge/Makefile
++++ vg/deps/gfakluge/Makefile
@@ -1,5 +1,5 @@
CXX?=g++
-CXXFLAGS:=-O3 -pipe -fPIC -march=native -mtune=native -std=c++11 -g -ggdb
-+CXXFLAGS:=-O3 -pipe -fPIC -std=c++11 -g -ggdb
++CXXFLAGS += -O3 -pipe -fPIC -Wall -std=c++11 -ggdb
PREFIX=/usr/local
# We want to pass -Wa,-q to GCC use the Clang assembler, but Apple Clang can't take that
-@@ -21,10 +21,10 @@ LD_LIB_FLAGS=-L./src/ -L./
+@@ -21,10 +21,10 @@
LD_INC_FLAGS=-I./src/ -I./ -I./src/tinyFA -I./$(BUILD_DIR)
gfak: $(BUILD_DIR)/main.o src/gfakluge.hpp src/tinyFA/pliib.hpp src/tinyFA/tinyfa.hpp | $(BUILD_DIR) $(BIN_DIR)
@@ -280,13 +280,13 @@ So that Debian can pass hardening flags
$(BUILD_DIR)/main.o: src/main.cpp src/gfakluge.hpp src/tinyFA/pliib.hpp src/tinyFA/tinyfa.hpp | $(BUILD_DIR) $(BIN_DIR)
- +$(CXX) $(CXXFLAGS) -c -o $@ $< $(LD_LIB_FLAGS) $(LD_INC_FLAGS)
-+ +$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $< $(LD_LIB_FLAGS) $(LD_INC_FLAGS)
++ +$(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $< $(LD_LIB_FLAGS) $(LD_INC_FLAGS)
$(BUILD_DIR):
mkdir -p $(BUILD_DIR)
---- a/deps/htslib/Makefile
-+++ b/deps/htslib/Makefile
-@@ -33,9 +33,9 @@ CPPFLAGS =
+--- vg.orig/deps/htslib/Makefile
++++ vg/deps/htslib/Makefile
+@@ -33,9 +33,9 @@
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
@@ -298,9 +298,9 @@ So that Debian can pass hardening flags
LIBS = $(htslib_default_libs)
prefix = /usr/local
---- a/deps/vcflib/Makefile
-+++ b/deps/vcflib/Makefile
-@@ -135,7 +135,7 @@ HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixp
+--- vg.orig/deps/vcflib/Makefile
++++ vg/deps/vcflib/Makefile
+@@ -135,7 +135,7 @@
INCLUDES = $(shell pkg-config --cflags libfastahack) $(HTS_INCLUDES) -I$(INC_DIR)
@@ -309,7 +309,7 @@ So that Debian can pass hardening flags
all: $(OBJECTS) $(BINS) scriptToBin
-@@ -144,9 +144,7 @@ scriptToBin: $(BINS)
+@@ -144,9 +144,7 @@
GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
@@ -320,7 +320,7 @@ So that Debian can pass hardening flags
openmp:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
-@@ -158,7 +156,8 @@ gprof:
+@@ -158,7 +156,8 @@
$(MAKE) CXXFLAGS="$(CXXFLAGS)" all
$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
@@ -330,7 +330,7 @@ So that Debian can pass hardening flags
multichoose: pre
cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-@@ -167,7 +166,7 @@ intervaltree: pre
+@@ -167,7 +166,7 @@
cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
$(TABIX): pre
@@ -339,7 +339,7 @@ So that Debian can pass hardening flags
$(SMITHWATERMAN): pre
cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
-@@ -190,7 +189,7 @@ $(SHORTBINS): pre
+@@ -190,7 +189,7 @@
$(MAKE) bin/$@
$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(FILEVERCMP) pre intervaltree
@@ -348,8 +348,8 @@ So that Debian can pass hardening flags
libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(FILEVERCMP) $(TABIX) pre
ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(FILEVERCMP) $(TABIX)
---- a/deps/vcflib/intervaltree/Makefile
-+++ b/deps/vcflib/intervaltree/Makefile
+--- vg.orig/deps/vcflib/intervaltree/Makefile
++++ vg/deps/vcflib/intervaltree/Makefile
@@ -8,7 +8,7 @@
# FreeBSD ports, MacPorts, pkgsrc, etc.)
@@ -359,7 +359,7 @@ So that Debian can pass hardening flags
DESTDIR ?= stage
PREFIX ?= /usr/local
MKDIR ?= mkdir
-@@ -20,7 +20,7 @@ BIN = interval_tree_test
+@@ -20,7 +20,7 @@
all: ${BIN}
${BIN}: interval_tree_test.cpp IntervalTree.h
@@ -368,9 +368,9 @@ So that Debian can pass hardening flags
install: all
${MKDIR} -p ${DESTDIR}${PREFIX}/bin
---- a/deps/vcflib/tabixpp/Makefile
-+++ b/deps/vcflib/tabixpp/Makefile
-@@ -32,18 +32,17 @@ all-recur lib-recur clean-recur cleanloc
+--- vg.orig/deps/vcflib/tabixpp/Makefile
++++ vg/deps/vcflib/tabixpp/Makefile
+@@ -32,18 +32,17 @@
all: $(PROG)
tabix.o: $(HTS_HEADERS) tabix.cpp tabix.hpp
@@ -391,9 +391,9 @@ So that Debian can pass hardening flags
- cd htslib && $(MAKE) clean
clean:cleanlocal-recur
---- a/deps/sonLib/C/Makefile
-+++ b/deps/sonLib/C/Makefile
-@@ -12,7 +12,7 @@ quickTreeLibPath = ../externalTools/quic
+--- vg.orig/deps/sonLib/C/Makefile
++++ vg/deps/sonLib/C/Makefile
+@@ -12,7 +12,7 @@
testProgs = ${binPath}/sonLibTests ${binPath}/sonLib_kvDatabaseTest ${binPath}/sonLib_cigarTest ${binPath}/sonLib_fastaCTest
@@ -402,7 +402,7 @@ So that Debian can pass hardening flags
cppflags += ${kyotoTycoonIncl}
all : ${libPath}/sonLib.a ${testProgs}
-@@ -22,27 +22,27 @@ clean :
+@@ -22,27 +22,27 @@
${binPath}/sonLibTests : ${libTests} ${libInternalHeaders} ${libPath}/sonLib.a ${libPath}/cuTest.a tests/allTests.c
@mkdir -p $(dir $@)
@@ -435,7 +435,7 @@ So that Debian can pass hardening flags
mv $@.tmp $@
${libPath}/%.h: inc/%.h
-@@ -52,8 +52,8 @@ ${libPath}/%.h: inc/%.h
+@@ -52,8 +52,8 @@
${libPath}/sonLib.a : ${libSources} ${cppSources} $(foreach l, ${libHeaders}, ${libPath}/$(notdir $l)) ${libInternalHeaders}
@mkdir -p $(dir $@)
@@ -446,9 +446,9 @@ So that Debian can pass hardening flags
ar rc sonLib.a *.o ${quickTreeObjects}
ranlib sonLib.a
rm *.o
---- a/deps/sublinear-Li-Stephens/makefile
-+++ b/deps/sublinear-Li-Stephens/makefile
-@@ -9,7 +9,7 @@ LIB_DIR:= $(CWD)/lib
+--- vg.orig/deps/sublinear-Li-Stephens/makefile
++++ vg/deps/sublinear-Li-Stephens/makefile
+@@ -9,7 +9,7 @@
DEP_DIR:= $(CWD)/deps
CXX:=g++
@@ -457,7 +457,7 @@ So that Debian can pass hardening flags
ifeq ($(INCLUDE_FLAGS),)
# Include flags may be set by library user
-@@ -42,89 +42,89 @@ clean:
+@@ -42,89 +42,89 @@
rm -f $(BIN_DIR)/* $(OBJ_DIR)/*.o $(TEST_OBJ_DIR)/*.o $(LIB_DIR)/*
tests : $(TEST_OBJ_DIR)/test.o $(CORE_OBJ) $(LIBHTS)
@@ -573,9 +573,9 @@ So that Debian can pass hardening flags
$(LIBHTS) :
cd deps/htslib && make
---- a/deps/vcflib/multichoose/Makefile
-+++ b/deps/vcflib/multichoose/Makefile
-@@ -8,13 +8,13 @@ all: multichoose multipermute
+--- vg.orig/deps/vcflib/multichoose/Makefile
++++ vg/deps/vcflib/multichoose/Makefile
+@@ -8,13 +8,13 @@
# ${CXX} multichoose_recursive.cpp -o multichoose_recursive
multichoose: multichoose.cpp multichoose.h
@@ -592,9 +592,9 @@ So that Debian can pass hardening flags
clean:
rm -f cmultichoose
---- a/deps/vcflib/filevercmp/Makefile
-+++ b/deps/vcflib/filevercmp/Makefile
-@@ -7,7 +7,7 @@ clean:
+--- vg.orig/deps/vcflib/filevercmp/Makefile
++++ vg/deps/vcflib/filevercmp/Makefile
+@@ -7,7 +7,7 @@
.PHONY: all clean
filevercmp.o: filevercmp.c main.c filevercmp.h
@@ -604,9 +604,9 @@ So that Debian can pass hardening flags
filevercmp: filevercmp.o
- gcc -o filevercmp main.c filevercmp.o
+ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o filevercmp main.c filevercmp.o
---- a/deps/libvgio/CMakeLists.txt
-+++ b/deps/libvgio/CMakeLists.txt
-@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.9)
+--- vg.orig/deps/libvgio/CMakeLists.txt
++++ vg/deps/libvgio/CMakeLists.txt
+@@ -2,7 +2,7 @@
project(libvgio VERSION 0.0.0 LANGUAGES CXX)
# Optimize by default, but also include debug info
@@ -615,9 +615,9 @@ So that Debian can pass hardening flags
# Use C++14, so that Protobuf headers that use lambdas will work.
set(CMAKE_CXX_STANDARD 14)
---- a/deps/gbwt/Makefile
-+++ b/deps/gbwt/Makefile
-@@ -45,28 +45,28 @@ OBSOLETE=prepare_text prepare_text.o met
+--- vg.orig/deps/gbwt/Makefile
++++ vg/deps/gbwt/Makefile
+@@ -45,28 +45,28 @@
all:$(LIBRARY) $(PROGRAMS)
%.o:%.cpp $(HEADERS)
@@ -653,9 +653,72 @@ So that Debian can pass hardening flags
clean:
rm -f $(PROGRAMS) $(OBJS) $(LIBRARY) $(OBSOLETE)
---- a/deps/sdsl-lite/CMakeLists.txt
-+++ b/deps/sdsl-lite/CMakeLists.txt
-@@ -118,7 +118,6 @@ else()
+--- vg.orig/deps/libbdsg/Makefile
++++ vg/deps/libbdsg/Makefile
+@@ -36,47 +36,47 @@
+ -include .pre-build
+
+ $(OBJ_DIR)/eades_algorithm.o: $(SRC_DIR)/eades_algorithm.cpp $(INC_DIR)/bdsg/eades_algorithm.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/eades_algorithm.cpp -o $(OBJ_DIR)/eades_algorithm.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/eades_algorithm.cpp -o $(OBJ_DIR)/eades_algorithm.o
+
+ $(OBJ_DIR)/hash_graph.o: $(SRC_DIR)/hash_graph.cpp $(INC_DIR)/bdsg/hash_graph.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/hash_graph.cpp -o $(OBJ_DIR)/hash_graph.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/hash_graph.cpp -o $(OBJ_DIR)/hash_graph.o
+
+ $(OBJ_DIR)/is_single_stranded.o: $(SRC_DIR)/is_single_stranded.cpp $(INC_DIR)/bdsg/is_single_stranded.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/is_single_stranded.cpp -o $(OBJ_DIR)/is_single_stranded.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/is_single_stranded.cpp -o $(OBJ_DIR)/is_single_stranded.o
+
+ $(OBJ_DIR)/node.o: $(SRC_DIR)/node.cpp $(INC_DIR)/bdsg/node.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/node.cpp -o $(OBJ_DIR)/node.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/node.cpp -o $(OBJ_DIR)/node.o
+
+ $(OBJ_DIR)/odgi.o: $(SRC_DIR)/odgi.cpp $(INC_DIR)/bdsg/odgi.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/odgi.cpp -o $(OBJ_DIR)/odgi.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/odgi.cpp -o $(OBJ_DIR)/odgi.o
+
+ $(OBJ_DIR)/packed_graph.o: $(SRC_DIR)/packed_graph.cpp $(INC_DIR)/bdsg/packed_graph.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/packed_graph.cpp -o $(OBJ_DIR)/packed_graph.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/packed_graph.cpp -o $(OBJ_DIR)/packed_graph.o
+
+ $(OBJ_DIR)/packed_structs.o: $(SRC_DIR)/packed_structs.cpp $(INC_DIR)/bdsg/packed_structs.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/packed_structs.cpp -o $(OBJ_DIR)/packed_structs.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/packed_structs.cpp -o $(OBJ_DIR)/packed_structs.o
+
+ $(OBJ_DIR)/path_position_overlays.o: $(SRC_DIR)/path_position_overlays.cpp $(INC_DIR)/bdsg/path_position_overlays.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/path_position_overlays.cpp -o $(OBJ_DIR)/path_position_overlays.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/path_position_overlays.cpp -o $(OBJ_DIR)/path_position_overlays.o
+
+ $(OBJ_DIR)/packed_path_position_overlays.o: $(SRC_DIR)/packed_path_position_overlays.cpp $(INC_DIR)/bdsg/packed_path_position_overlays.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/packed_path_position_overlays.cpp -o $(OBJ_DIR)/packed_path_position_overlays.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/packed_path_position_overlays.cpp -o $(OBJ_DIR)/packed_path_position_overlays.o
+
+ $(OBJ_DIR)/vectorizable_overlays.o: $(SRC_DIR)/vectorizable_overlays.cpp $(INC_DIR)/bdsg/vectorizable_overlays.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/vectorizable_overlays.cpp -o $(OBJ_DIR)/vectorizable_overlays.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/vectorizable_overlays.cpp -o $(OBJ_DIR)/vectorizable_overlays.o
+
+ $(OBJ_DIR)/split_strand_graph.o: $(SRC_DIR)/split_strand_graph.cpp $(INC_DIR)/bdsg/split_strand_graph.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/split_strand_graph.cpp -o $(OBJ_DIR)/split_strand_graph.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/split_strand_graph.cpp -o $(OBJ_DIR)/split_strand_graph.o
+
+ $(OBJ_DIR)/utility.o: $(SRC_DIR)/utility.cpp $(INC_DIR)/bdsg/utility.hpp
+- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/utility.cpp -o $(OBJ_DIR)/utility.o
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/utility.cpp -o $(OBJ_DIR)/utility.o
+
+ $(LIB_DIR)/libbdsg.a: $(OBJS)
+ rm -f $@
+ ar rs $@ $(OBJS)
+
+ $(BIN_DIR)/test_libbdsg: $(LIB_DIR)/libbdsg.a $(SRC_DIR)/test_libbdsg.cpp
+- $(CXX) $(CXXFLAGS) -L $(LIB_DIR) $(LIB_FLAGS) $(SRC_DIR)/test_libbdsg.cpp -o $(BIN_DIR)/test_libbdsg
++ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -L $(LIB_DIR) $(LIB_FLAGS) $(SRC_DIR)/test_libbdsg.cpp -o $(BIN_DIR)/test_libbdsg
+ chmod +x $(BIN_DIR)/test_libbdsg
+
+ install: $(LIB_DIR)/libbdsg.a
+--- vg.orig/deps/sdsl-lite/CMakeLists.txt
++++ vg/deps/sdsl-lite/CMakeLists.txt
+@@ -118,7 +118,6 @@
message(WARNING "git not found. Cloning of submodules will not work.")
endif()
@@ -663,8 +726,8 @@ So that Debian can pass hardening flags
add_subdirectory(include)
add_subdirectory(lib)
---- a/deps/sdsl-lite/lib/CMakeLists.txt
-+++ b/deps/sdsl-lite/lib/CMakeLists.txt
+--- vg.orig/deps/sdsl-lite/lib/CMakeLists.txt
++++ vg/deps/sdsl-lite/lib/CMakeLists.txt
@@ -1,6 +1,5 @@
include_directories(#"${CMAKE_CURRENT_SOURCE_DIR}/../include"
"${CMAKE_CURRENT_BINARY_DIR}/../include"
@@ -672,9 +735,9 @@ So that Debian can pass hardening flags
)
---- 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 cha
+--- vg.orig/deps/sdsl-lite/lib/structure_tree.cpp.cmake
++++ vg/deps/sdsl-lite/lib/structure_tree.cpp.cmake
+@@ -45,7 +45,7 @@
<< " <head>\n"
<< " <meta http-equiv=\"Content-Type\" content=\"text/html;charset=utf-8\">\n"
<< " <title>" << file_name << "</title>\n"
@@ -683,9 +746,9 @@ So that Debian can pass hardening flags
<< " <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"
---- a/deps/pinchesAndCacti/Makefile
-+++ b/deps/pinchesAndCacti/Makefile
-@@ -9,10 +9,10 @@ testBin = tests/testBin
+--- vg.orig/deps/pinchesAndCacti/Makefile
++++ vg/deps/pinchesAndCacti/Makefile
+@@ -9,10 +9,10 @@
all : externalToolsM ${libPath}/stPinchesAndCacti.a ${binPath}/stPinchesAndCactiTests
externalToolsM :
@@ -698,7 +761,7 @@ So that Debian can pass hardening flags
ar rc stPinchesAndCacti.a *.o
ranlib stPinchesAndCacti.a
rm *.o
-@@ -20,10 +20,10 @@ ${libPath}/stPinchesAndCacti.a : ${libSo
+@@ -20,10 +20,10 @@
cp ${libHeaders} ${libPath}/
${binPath}/stPinchesAndCactiTests : ${libTests} ${libSources} ${libHeaders} ${basicLibsDependencies} externalToolsM
@@ -711,9 +774,9 @@ So that Debian can pass hardening flags
rm -f *.o
rm -f ${libPath}/stPinchesAndCacti.a ${binPath}/stPinchesAndCactiTests
---- a/deps/pinchesAndCacti/externalTools/threeEdgeConnected/Makefile
-+++ b/deps/pinchesAndCacti/externalTools/threeEdgeConnected/Makefile
-@@ -8,7 +8,7 @@ libTests = tests/*.c
+--- vg.orig/deps/pinchesAndCacti/externalTools/threeEdgeConnected/Makefile
++++ vg/deps/pinchesAndCacti/externalTools/threeEdgeConnected/Makefile
+@@ -8,7 +8,7 @@
all : ${libPath}/3EdgeConnected.a ${binPath}/3EdgeTests
${libPath}/3EdgeConnected.a : ${libSources} ${libHeaders} ${basicLibsDependencies}
@@ -722,15 +785,15 @@ So that Debian can pass hardening flags
ar rc 3EdgeConnected.a *.o
ranlib 3EdgeConnected.a
rm *.o
-@@ -19,4 +19,4 @@ clean :
+@@ -19,4 +19,4 @@
rm -f ${libPath}/3EdgeConnected.a ${binPath}/3EdgeTests
${binPath}/3EdgeTests : ${libTests} ${libSources} ${libHeaders} ${libPath}/3EdgeConnected.a ${basicLibsDependencies}
- ${cxx} ${cflags} -I inc -I${libPath} -o ${binPath}/3EdgeTests ${libTests} ${libPath}/3EdgeConnected.a ${basicLibs}
+ ${cxx} $(LDFLAGS) $(CPPFLAGS) ${cflags} $(CFLAGS) -I inc -I${libPath} -o ${binPath}/3EdgeTests ${libTests} ${libPath}/3EdgeConnected.a ${basicLibs}
---- a/deps/sonLib/Makefile
-+++ b/deps/sonLib/Makefile
-@@ -9,16 +9,16 @@ clean : cP.clean externalToolsP.clean
+--- vg.orig/deps/sonLib/Makefile
++++ vg/deps/sonLib/Makefile
+@@ -9,16 +9,16 @@
rm -f ${binPath}/sonLib_daemonize.py
cP: externalToolsP
@@ -751,58 +814,3 @@ So that Debian can pass hardening flags
test : all
PYTHONPATH=.. PATH=../../bin:$$PATH python allTests.py --testLength=SHORT --logLevel=CRITICAL
---- a/deps/libbdsg/Makefile
-+++ b/deps/libbdsg/Makefile
-@@ -36,40 +36,40 @@ test: all $(BIN_DIR)/test_libbdsg
- -include .pre-build
-
- $(OBJ_DIR)/eades_algorithm.o: $(SRC_DIR)/eades_algorithm.cpp $(INC_DIR)/bdsg/eades_algorithm.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/eades_algorithm.cpp -o $(OBJ_DIR)/eades_algorithm.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/eades_algorithm.cpp -o $(OBJ_DIR)/eades_algorithm.o
-
- $(OBJ_DIR)/hash_graph.o: $(SRC_DIR)/hash_graph.cpp $(INC_DIR)/bdsg/hash_graph.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/hash_graph.cpp -o $(OBJ_DIR)/hash_graph.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/hash_graph.cpp -o $(OBJ_DIR)/hash_graph.o
-
- $(OBJ_DIR)/is_single_stranded.o: $(SRC_DIR)/is_single_stranded.cpp $(INC_DIR)/bdsg/is_single_stranded.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/is_single_stranded.cpp -o $(OBJ_DIR)/is_single_stranded.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/is_single_stranded.cpp -o $(OBJ_DIR)/is_single_stranded.o
-
- $(OBJ_DIR)/node.o: $(SRC_DIR)/node.cpp $(INC_DIR)/bdsg/node.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/node.cpp -o $(OBJ_DIR)/node.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/node.cpp -o $(OBJ_DIR)/node.o
-
- $(OBJ_DIR)/odgi.o: $(SRC_DIR)/odgi.cpp $(INC_DIR)/bdsg/odgi.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/odgi.cpp -o $(OBJ_DIR)/odgi.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/odgi.cpp -o $(OBJ_DIR)/odgi.o
-
- $(OBJ_DIR)/packed_graph.o: $(SRC_DIR)/packed_graph.cpp $(INC_DIR)/bdsg/packed_graph.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/packed_graph.cpp -o $(OBJ_DIR)/packed_graph.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/packed_graph.cpp -o $(OBJ_DIR)/packed_graph.o
-
- $(OBJ_DIR)/packed_structs.o: $(SRC_DIR)/packed_structs.cpp $(INC_DIR)/bdsg/packed_structs.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/packed_structs.cpp -o $(OBJ_DIR)/packed_structs.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/packed_structs.cpp -o $(OBJ_DIR)/packed_structs.o
-
- $(OBJ_DIR)/path_position_overlays.o: $(SRC_DIR)/path_position_overlays.cpp $(INC_DIR)/bdsg/path_position_overlays.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/path_position_overlays.cpp -o $(OBJ_DIR)/path_position_overlays.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/path_position_overlays.cpp -o $(OBJ_DIR)/path_position_overlays.o
-
- $(OBJ_DIR)/packed_path_position_overlays.o: $(SRC_DIR)/packed_path_position_overlays.cpp $(INC_DIR)/bdsg/packed_path_position_overlays.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/packed_path_position_overlays.cpp -o $(OBJ_DIR)/packed_path_position_overlays.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/packed_path_position_overlays.cpp -o $(OBJ_DIR)/packed_path_position_overlays.o
-
- $(OBJ_DIR)/vectorizable_overlays.o: $(SRC_DIR)/vectorizable_overlays.cpp $(INC_DIR)/bdsg/vectorizable_overlays.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/vectorizable_overlays.cpp -o $(OBJ_DIR)/vectorizable_overlays.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/vectorizable_overlays.cpp -o $(OBJ_DIR)/vectorizable_overlays.o
-
- $(OBJ_DIR)/split_strand_graph.o: $(SRC_DIR)/split_strand_graph.cpp $(INC_DIR)/bdsg/split_strand_graph.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/split_strand_graph.cpp -o $(OBJ_DIR)/split_strand_graph.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/split_strand_graph.cpp -o $(OBJ_DIR)/split_strand_graph.o
-
- $(OBJ_DIR)/utility.o: $(SRC_DIR)/utility.cpp $(INC_DIR)/bdsg/utility.hpp
-- $(CXX) $(CXXFLAGS) -c $(SRC_DIR)/utility.cpp -o $(OBJ_DIR)/utility.o
-+ $(CXX) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $(SRC_DIR)/utility.cpp -o $(OBJ_DIR)/utility.o
-
- $(LIB_DIR)/libbdsg.a: $(OBJS)
- rm -f $@
=====================================
debian/patches/no_need_for_snappy
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Due to other patches, snappy is no longer a dependency
---- a/Makefile
-+++ b/Makefile
-@@ -206,7 +206,6 @@ CONFIGURATION_OBJ =
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -206,7 +206,6 @@
LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
SDSL_DIR:=deps/sdsl-lite
@@ -10,7 +10,7 @@ Description: Due to other patches, snappy is no longer a dependency
GCSA2_DIR:=deps/gcsa2
GBWT_DIR:=deps/gbwt
GBWTGRAPH_DIR=deps/gbwtgraph
-@@ -248,7 +247,6 @@ DEP_OBJ += $(OBJ_DIR)/Fasta.o
+@@ -248,7 +247,6 @@
LIB_DEPS =
LIB_DEPS += $(LIB_DIR)/libsdsl.a
LIB_DEPS += $(LIB_DIR)/libssw.a
@@ -18,7 +18,7 @@ Description: Due to other patches, snappy is no longer a dependency
LIB_DEPS += $(LIB_DIR)/libgcsa2.a
LIB_DEPS += $(LIB_DIR)/libgbwt.a
LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
-@@ -366,11 +364,6 @@ endif
+@@ -366,11 +364,6 @@
$(LIB_DIR)/libssw.a: $(SSW_DIR)/*.c $(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)/$(LIB_DIR)
=====================================
debian/patches/no_pg
=====================================
@@ -1,7 +1,7 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Ensure that we don't accidentally include profile mode
---- a/deps/gfakluge/makefile.detuned
-+++ b/deps/gfakluge/makefile.detuned
+--- vg.orig/deps/gfakluge/makefile.detuned
++++ vg/deps/gfakluge/makefile.detuned
@@ -1,5 +1,5 @@
CXX?=g++
-CXXFLAGS:=-O0 -pipe -std=c++11 -pg -ggdb
@@ -9,9 +9,9 @@ Description: Ensure that we don't accidentally include profile mode
BIN_DIR:=bin
---- a/deps/sonLib/include.mk
-+++ b/deps/sonLib/include.mk
-@@ -54,7 +54,7 @@ cflags_ultraDbg = -Wall -Werror --pedant
+--- vg.orig/deps/sonLib/include.mk
++++ vg/deps/sonLib/include.mk
+@@ -54,7 +54,7 @@
cppflags_ultraDbg = -g -O1 -fno-inline -fno-omit-frame-pointer -fsanitize=address
#Profile flags
@@ -20,9 +20,9 @@ Description: Ensure that we don't accidentally include profile mode
#Flags to use
ifndef CGL_DEBUG
---- a/deps/vcflib/Makefile
-+++ b/deps/vcflib/Makefile
-@@ -158,7 +158,7 @@ profiling:
+--- vg.orig/deps/vcflib/Makefile
++++ vg/deps/vcflib/Makefile
+@@ -158,7 +158,7 @@
$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
gprof:
@@ -31,9 +31,9 @@ Description: Ensure that we don't accidentally include profile mode
$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
---- a/deps/vowpal_wabbit/Makefile
-+++ b/deps/vowpal_wabbit/Makefile
-@@ -103,7 +103,7 @@ vw:
+--- vg.orig/deps/vowpal_wabbit/Makefile
++++ vg/deps/vowpal_wabbit/Makefile
+@@ -103,7 +103,7 @@
cd vowpalwabbit; $(MAKE) -j $(NPROCS) things
#Target-specific flags for a profiling build. (Copied from line 70)
@@ -42,7 +42,7 @@ Description: Ensure that we don't accidentally include profile mode
vw_gcov: CXX = g++
vw_gcov:
cd vowpalwabbit && env LDFLAGS="-fprofile-arcs -ftest-coverage -lgcov"; $(MAKE) -j $(NPROCS) things
-@@ -115,7 +115,7 @@ library_example: vw
+@@ -115,7 +115,7 @@
cd library; $(MAKE) -j $(NPROCS) things
#Target-specific flags for a profiling build. (Copied from line 70)
=====================================
debian/patches/no_rpath
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: don't use rpath
---- a/Makefile
-+++ b/Makefile
-@@ -128,8 +128,6 @@ ifeq ($(shell uname -s),Darwin)
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -128,8 +128,6 @@
else
# We are not running on OS X
=====================================
debian/patches/parallize_better
=====================================
@@ -1,5 +1,5 @@
From: Michael R. Crusoe <michael.crusoe at gmail.com>
-Subject: improve build parallization
+Subject: improve build parallelization
--- vg.orig/deps/sonLib/externalTools/Makefile
+++ vg/deps/sonLib/externalTools/Makefile
@@ -8,13 +8,13 @@
=====================================
debian/patches/series
=====================================
@@ -18,8 +18,10 @@ use_packaged_fastahack
#use_packaged_htslib # waiting on https://github.com/samtools/htslib/pull/904/files or similiar to be merged & new htslib release
#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
+#use_packaged_protobuf ?
hardening_flags
use_packaged_smithwaterman
static
use_packaged_lz4
parallize_better
+use_packaged_libtsl-hopscotch-map-dev
=====================================
debian/patches/spelling
=====================================
@@ -1,8 +1,8 @@
From: Michael R. Crusoe <michael.crusoe at gmail.com>
Subject: fix spelling typos
---- a/src/unittest/genotypekit.cpp
-+++ b/src/unittest/genotypekit.cpp
-@@ -431,7 +431,7 @@ TEST_CASE("ExhaustiveTraversalFinder fin
+--- vg.orig/src/unittest/genotypekit.cpp
++++ vg/src/unittest/genotypekit.cpp
+@@ -431,7 +431,7 @@
REQUIRE(found_trav_2);
}
@@ -11,9 +11,9 @@ Subject: fix spelling typos
SECTION("Directed cycle does not count as ultrabubble") {
---- a/src/unittest/aligner.cpp
-+++ b/src/unittest/aligner.cpp
-@@ -123,7 +123,7 @@ TEST_CASE("Full-length bonus can hold do
+--- vg.orig/src/unittest/aligner.cpp
++++ vg/src/unittest/aligner.cpp
+@@ -123,7 +123,7 @@
aligner_1.align(aln1, graph, true, false);
aligner_2.align(aln2, graph, true, false);
@@ -22,7 +22,7 @@ Subject: fix spelling typos
REQUIRE(aln1.path().mapping_size() == 1);
REQUIRE(aln1.path().mapping(0).position().node_id() == n0->id());
REQUIRE(aln1.path().mapping(0).position().offset() == 2);
-@@ -158,7 +158,7 @@ TEST_CASE("Full-length bonus can hold do
+@@ -158,7 +158,7 @@
aligner_1.align(aln1, graph, true, false);
aligner_2.align(aln2, graph, true, false);
@@ -31,9 +31,9 @@ Subject: fix spelling typos
REQUIRE(aln1.path().mapping_size() == 1);
REQUIRE(aln1.path().mapping(0).position().node_id() == n0->id());
REQUIRE(aln1.path().mapping(0).position().offset() == 0);
---- a/src/subcommand/mod_main.cpp
-+++ b/src/subcommand/mod_main.cpp
-@@ -45,7 +45,7 @@ void help_mod(char** argv) {
+--- vg.orig/src/subcommand/mod_main.cpp
++++ vg/src/subcommand/mod_main.cpp
+@@ -45,7 +45,7 @@
<< " edges from old to new copies to convert the graph into a DAG" << endl
<< " until the shortest path through each SCC is N bases long" << endl
<< " -L, --dagify-len-max N stop a dagification step if the unrolling component has this much sequence" << endl
@@ -42,9 +42,9 @@ Subject: fix spelling typos
<< " component of the graph" << endl
<< " -O, --orient-forward orient the nodes in the graph forward" << endl
<< " -N, --remove-non-path keep only nodes and edges which are part of paths" << endl
---- a/src/subcommand/find_main.cpp
-+++ b/src/subcommand/find_main.cpp
-@@ -50,7 +50,7 @@ void help_find(char** argv) {
+--- vg.orig/src/subcommand/find_main.cpp
++++ vg/src/subcommand/find_main.cpp
+@@ -50,7 +50,7 @@
<< "sequences:" << endl
<< " -g, --gcsa FILE use this GCSA2 index of the sequence space of the graph" << endl
<< " -z, --kmer-size N split up --sequence into kmers of size N" << endl
@@ -53,9 +53,9 @@ Subject: fix spelling typos
<< " -S, --sequence STR search for sequence STR using --kmer-size kmers" << endl
<< " -M, --mems STR describe the super-maximal exact matches of the STR (gcsa2) in JSON" << endl
<< " -B, --reseed-length N find non-super-maximal MEMs inside SMEMs of length at least N" << endl
---- a/src/subcommand/genotype_main.cpp
-+++ b/src/subcommand/genotype_main.cpp
-@@ -34,7 +34,7 @@ void help_genotype(char** argv) {
+--- vg.orig/src/subcommand/genotype_main.cpp
++++ vg/src/subcommand/genotype_main.cpp
+@@ -34,7 +34,7 @@
<< " -A, --no_indel_realign disable indel realignment" << endl
<< " -d, --het_prior_denom denominator for prior probability of heterozygousness" << endl
<< " -P, --min_per_strand min unique reads per strand for a called allele to accept a call" << endl
@@ -64,9 +64,9 @@ Subject: fix spelling typos
<< " -T, --traversal traversal finder to use {reads, exhaustive, representative, adaptive} (adaptive)" << endl
<< " -p, --progress show progress" << endl
<< " -t, --threads N number of threads to use" << endl;
---- a/src/subcommand/gamcompare_main.cpp
-+++ b/src/subcommand/gamcompare_main.cpp
-@@ -23,7 +23,7 @@ void help_gamcompare(char** argv) {
+--- vg.orig/src/subcommand/gamcompare_main.cpp
++++ vg/src/subcommand/gamcompare_main.cpp
+@@ -23,7 +23,7 @@
<< endl
<< "options:" << endl
<< " -r, --range N distance within which to consider reads correct" << endl
@@ -75,9 +75,9 @@ Subject: fix spelling typos
<< " -a, --aligner aligner name for TSV output [\"vg\"]" << endl
<< " -t, --threads N number of threads to use" << endl;
}
---- a/src/subcommand/view_main.cpp
-+++ b/src/subcommand/view_main.cpp
-@@ -73,7 +73,7 @@ void help_view(char** argv) {
+--- vg.orig/src/subcommand/view_main.cpp
++++ vg/src/subcommand/view_main.cpp
+@@ -73,7 +73,7 @@
<< " -X, --fastq-out output fastq (input defaults to GAM)" << endl
<< " -i, --interleaved fastq is interleaved paired-ended" << endl
@@ -86,9 +86,9 @@ Subject: fix spelling typos
<< " -l, --pileup-in input VG Pileup format" << endl
<< " -R, --snarl-in input VG Snarl format" << endl
---- a/src/sampler.cpp
-+++ b/src/sampler.cpp
-@@ -603,7 +603,7 @@ NGSSimulator::NGSSimulator(PathPositionH
+--- vg.orig/src/sampler.cpp
++++ vg/src/sampler.cpp
+@@ -603,7 +603,7 @@
});
if (!source_paths.empty() && !transcript_expressions.empty()) {
@@ -97,9 +97,9 @@ Subject: fix spelling typos
exit(1);
}
---- a/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
-+++ b/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
-@@ -627,7 +627,7 @@ void parse_feature_tweaks(arguments& arg
+--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
++++ vg/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
+@@ -627,7 +627,7 @@
||
interactions_settings_doubled /*settings were restored from model file to file_options and overriden by params from command line*/)
{
@@ -108,9 +108,9 @@ Subject: fix spelling typos
// in case arrays were already filled in with values from old model file - reset them
if (!arg.all->pairs.empty()) arg.all->pairs.clear();
---- a/deps/vowpal_wabbit/vowpalwabbit/global_data.h
-+++ b/deps/vowpal_wabbit/vowpalwabbit/global_data.h
-@@ -160,7 +160,7 @@ public:
+--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/global_data.h
++++ vg/deps/vowpal_wabbit/vowpalwabbit/global_data.h
+@@ -160,7 +160,7 @@
uint64_t hash = uniform_hash((unsigned char*)l.begin, l.end-l.begin, 378401);
uint64_t id = name2id.get(l, hash);
if (id != 0) // TODO: memory leak: char* temp
@@ -119,9 +119,9 @@ Subject: fix spelling typos
size_t len = l.end - l.begin;
substring l_copy = { calloc_or_throw<char>(len), nullptr };
memcpy(l_copy.begin, l.begin, len * sizeof(char));
---- a/src/index.cpp
-+++ b/src/index.cpp
-@@ -2140,7 +2140,7 @@ pair<int64_t, int64_t> Index::compare_km
+--- vg.orig/src/index.cpp
++++ vg/src/index.cpp
+@@ -2140,7 +2140,7 @@
string kmer;
parse_kmer(key, value, kmer, id, pos);
@@ -130,9 +130,9 @@ Subject: fix spelling typos
if (kmer != prev_kmer) {
string remk = reverse_complement(kmer);
---- a/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
-+++ b/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
-@@ -23,7 +23,7 @@ void name_value(substring &s, v_array<su
+--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
++++ vg/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
+@@ -23,7 +23,7 @@
THROW("error NaN value for: " << name[0]);
break;
default:
=====================================
debian/patches/static
=====================================
@@ -1,20 +1,20 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: For Debian, don't statically link to cairo, jansson, libstdc++, libgcc
---- a/Makefile
-+++ b/Makefile
-@@ -36,9 +36,9 @@ INCLUDE_FLAGS:=$(shell pkg-config --cfla
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -36,9 +36,9 @@
# Define libraries to link against. Make sure to always link statically against
# htslib and libdeflate and Protobuf so that we can use position-dependent code
# there for speed.
--LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
-+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lz -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
+-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
++LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lz -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
# Use pkg-config to find Cairo and all the libs it uses
-LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
+LD_LIB_FLAGS += $(shell pkg-config --libs cairo jansson)
# Travis needs -latomic for all builds *but* GCC on Mac
ifeq ($(strip $(shell $(CXX) -latomic /dev/null -o/dev/null 2>&1 | grep latomic | wc -l)), 0)
-@@ -181,7 +181,7 @@ LD_LIB_FLAGS += -lrocksdb -lbz2
+@@ -181,7 +181,7 @@
# 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?
=====================================
debian/patches/use_packaged_boost
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian packages of boost-program-options
---- a/Makefile
-+++ b/Makefile
-@@ -231,7 +231,6 @@ STRUCTURES_DIR:=deps/structures
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -231,7 +231,6 @@
BACKWARD_CPP_DIR:=deps/backward-cpp
DOZEU_DIR:=deps/dozeu
ELFUTILS_DIR:=deps/elfutils
@@ -10,7 +10,7 @@ Description: Use the Debian packages of boost-program-options
VOWPALWABBIT_DIR:=deps/vowpal_wabbit
LIBVGIO_DIR:=deps/libvgio
LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
-@@ -273,7 +272,6 @@ LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
+@@ -273,7 +272,6 @@
LIB_DEPS += $(LIB_DIR)/libstructures.a
LIB_DEPS += $(LIB_DIR)/libvw.a
LIB_DEPS += $(LIB_DIR)/liballreduce.a
@@ -18,7 +18,7 @@ Description: Use the Debian packages of boost-program-options
LIB_DEPS += $(LIB_DIR)/libvgio.a
LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
LIB_DEPS += $(LIB_DIR)/libbdsg.a
-@@ -538,14 +536,14 @@ $(LIB_DIR)/libstructures.a: $(STRUCTURES
+@@ -539,14 +537,14 @@
# if it doesn't find it, so let it fail.
# Also, we need to make sure nothing about -fopenmp makes it into the build, in case we are on Clang.
# vw doesn't need OpenMP
@@ -35,7 +35,7 @@ Description: Use the Debian packages of boost-program-options
+. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" $(MAKE) $(FILTER)
+. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a $(CWD)/$(LIB_DIR)/
+. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && mkdir -p $(CWD)/$(INC_DIR)/vowpalwabbit
-@@ -553,17 +551,6 @@ $(LIB_DIR)/libvw.a: $(LIB_DIR)/libboost_
+@@ -554,17 +552,6 @@
$(LIB_DIR)/liballreduce.a: $(LIB_DIR)/libvw.a
=====================================
debian/patches/use_packaged_elfutils
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian packages for elfutils
---- a/Makefile
-+++ b/Makefile
-@@ -135,7 +135,7 @@ else
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -135,7 +135,7 @@
LD_LIB_FLAGS += -rdynamic
# We want to link against the elfutils libraries
@@ -11,7 +11,7 @@ Description: Use the Debian packages for elfutils
# We get OpenMP the normal way, using whatever the compiler knows about
CXXFLAGS += -fopenmp
-@@ -225,7 +225,6 @@ SSW_DIR:=deps/ssw/src
+@@ -225,7 +225,6 @@
LINLS_DIR:=deps/sublinear-Li-Stephens
STRUCTURES_DIR:=deps/structures
DOZEU_DIR:=deps/dozeu
@@ -19,7 +19,7 @@ Description: Use the Debian packages for elfutils
VOWPALWABBIT_DIR:=deps/vowpal_wabbit
LIBVGIO_DIR:=deps/libvgio
LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
-@@ -270,15 +269,6 @@ LIB_DEPS += $(LIB_DIR)/libvgio.a
+@@ -270,15 +269,6 @@
LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
LIB_DEPS += $(LIB_DIR)/libbdsg.a
LIB_DEPS += $(LIB_DIR)/libxg.a
@@ -35,7 +35,7 @@ Description: Use the Debian packages for elfutils
# common dependencies to build before all vg src files
DEPS = $(LIB_DEPS)
-@@ -543,10 +533,6 @@ $(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hp
+@@ -544,27 +534,6 @@
$(INC_DIR)/dozeu/dozeu.h: $(DOZEU_DIR)/*.h
+mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/
@@ -43,6 +43,23 @@ Description: Use the Debian packages for elfutils
-
-$(LIB_DIR)/libdw.a: $(LIB_DIR)/libelf.a
-
- $(LIB_DIR)/libdwelf.a: $(LIB_DIR)/libelf.a
+-$(LIB_DIR)/libdwelf.a: $(LIB_DIR)/libelf.a
+-
+-$(LIB_DIR)/libdwfl.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.
+-$(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
+- +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 --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)/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)/
+-
+ $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
+ +$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -c -o $@ $< $(FILTER)
- $(LIB_DIR)/libdwfl.a: $(LIB_DIR)/libelf.a
=====================================
debian/patches/use_packaged_fastahack
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian version of fastahack; not working due to vg needing modifications to the upstream sourcecode
---- a/Makefile
-+++ b/Makefile
-@@ -31,12 +31,12 @@ include $(wildcard $(UNITTEST_OBJ_DIR)/*
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -31,12 +31,12 @@
CXXFLAGS := -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP $(CXXFLAGS)
# Set include flags. All -I options need to go in here, so the first directory listed is genuinely searched first.
@@ -13,11 +13,11 @@ Description: Use the Debian version of fastahack; not working due to vg needing
# htslib and libdeflate and Protobuf so that we can use position-dependent code
# there for speed.
-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph
-+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack)
++LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack)
# Use pkg-config to find Cairo and all the libs it uses
LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
-@@ -208,7 +208,6 @@ GCSA2_DIR:=deps/gcsa2
+@@ -208,7 +208,6 @@
GBWT_DIR:=deps/gbwt
GBWTGRAPH_DIR=deps/gbwtgraph
PROGRESS_BAR_DIR:=deps/progress_bar
@@ -25,7 +25,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
HTSLIB_DIR:=deps/htslib
VCFLIB_DIR:=deps/vcflib
GSSW_DIR:=deps/gssw
-@@ -232,7 +231,6 @@ BBHASH_DIR=deps/BBHash
+@@ -232,7 +231,6 @@
DEP_OBJ =
DEP_OBJ += $(OBJ_DIR)/progress_bar.o
DEP_OBJ += $(OBJ_DIR)/sha1.o
@@ -33,7 +33,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
# These are libraries that we need to build before we link vg.
-@@ -247,7 +245,6 @@ LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
+@@ -247,7 +245,6 @@
LIB_DEPS += $(LIB_DIR)/libhts.a
LIB_DEPS += $(LIB_DIR)/libvcflib.a
LIB_DEPS += $(LIB_DIR)/libgssw.a
@@ -41,16 +41,16 @@ Description: Use the Debian version of fastahack; not working due to vg needing
LIB_DEPS += $(LIB_DIR)/libsonlib.a
LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
-@@ -320,7 +317,7 @@ get-deps:
+@@ -320,7 +317,7 @@
# And we have submodule deps to build
deps: $(DEPS)
-test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(VCFLIB_DIR)/bin/vcf2tsv $(FASTAHACK_DIR)/fastahack
-+test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(VCFLIB_DIR)/bin/vcf2tsv
++test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(VCFLIB_DIR)/bin/vcf2tsv
. ./source_me.sh && cd test && prove -v t
docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp
-@@ -389,9 +386,6 @@ $(INC_DIR)/progress_bar.hpp: $(PROGRESS_
+@@ -389,9 +386,6 @@
$(OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/*.hpp $(PROGRESS_BAR_DIR)/*.cpp
+. ./source_me.sh && cd $(PROGRESS_BAR_DIR) && $(MAKE) $(FILTER) && cp progress_bar.o $(CWD)/$(OBJ_DIR)
@@ -60,7 +60,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
# 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.
-@@ -426,9 +420,6 @@ $(LIB_DIR)/libvcflib.a: $(LIB_DIR)/libht
+@@ -427,9 +421,6 @@
$(VCFLIB_DIR)/bin/vcf2tsv: $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.h $(LIB_DIR)/libvcflib.a
+. ./source_me.sh && cd $(VCFLIB_DIR) && HTS_LIB="$(CWD)/$(LIB_DIR)/libhts.a" HTS_INCLUDES="-I$(CWD)/$(INC_DIR)" HTS_LDFLAGS="-L$(CWD)/$(LIB_DIR) $(START_STATIC) -lhts -ldeflate $(END_STATIC) -lpthread -lm -lbz2 -llzma -lz" $(MAKE) vcf2tsv $(FILTER)
@@ -70,7 +70,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
$(LIB_DIR)/libgssw.a: $(GSSW_DIR)/src/gssw.c $(GSSW_DIR)/src/gssw.h
+. ./source_me.sh && cd $(GSSW_DIR) && $(MAKE) $(FILTER) && cp lib/* $(CWD)/$(LIB_DIR)/ && cp obj/* $(CWD)/$(OBJ_DIR) && cp src/*.h $(CWD)/$(INC_DIR)
-@@ -447,10 +438,6 @@ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMI
+@@ -448,10 +439,6 @@
$(INC_DIR)/sparsepp/spp.h:
+cp -r $(SPARSEPP_DIR)/sparsepp $(INC_DIR)/
@@ -81,7 +81,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
$(INC_DIR)/gfakluge.hpp: $(DEP_DIR)/gfakluge/src/gfakluge.hpp
+cp $(DEP_DIR)/gfakluge/src/*.hpp $(CWD)/$(INC_DIR)/ && cp $(DEP_DIR)/gfakluge/src/tinyFA/*.hpp $(CWD)/$(INC_DIR)/
-@@ -659,14 +646,12 @@ clean: clean-vcflib
+@@ -643,14 +630,12 @@
$(RM) -r share/
cd $(DEP_DIR) && cd sonLib && $(MAKE) clean
cd $(DEP_DIR) && cd htslib && $(MAKE) clean
@@ -96,15 +96,15 @@ Description: Use the Debian version of fastahack; not working due to vg needing
cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
cd $(DEP_DIR) && cd gfakluge && $(MAKE) clean
cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
-@@ -686,5 +671,4 @@ clean-rocksdb:
+@@ -664,5 +649,4 @@
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
---- a/test/Makefile
-+++ b/test/Makefile
-@@ -7,15 +7,12 @@ vg:=../bin/vg
+--- vg.orig/test/Makefile
++++ vg/test/Makefile
+@@ -7,15 +7,12 @@
all: test clean
@@ -121,9 +121,9 @@ Description: Use the Debian version of fastahack; not working due to vg needing
$(vg):
cd .. && $(MAKE) bin/vg
---- a/test/t/02_vg_construct.t
-+++ b/test/t/02_vg_construct.t
-@@ -75,7 +75,7 @@ rm -f fail.vg
+--- vg.orig/test/t/02_vg_construct.t
++++ vg/test/t/02_vg_construct.t
+@@ -75,7 +75,7 @@
# check that we produce a full graph
@@ -132,9 +132,9 @@ Description: Use the Debian version of fastahack; not working due to vg needing
variantbp=$(zcat < small/x.vcf.gz | ../deps/vcflib/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); } }' \
---- a/deps/vcflib/Makefile
-+++ b/deps/vcflib/Makefile
-@@ -119,7 +119,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
+--- vg.orig/deps/vcflib/Makefile
++++ vg/deps/vcflib/Makefile
+@@ -119,7 +119,6 @@
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
TABIX = tabixpp/tabix.o
@@ -142,7 +142,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
REPEATS = smithwaterman/Repeats.o
INDELALLELE = smithwaterman/IndelAllele.o
-@@ -135,10 +134,8 @@ HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabix
+@@ -135,10 +134,8 @@
HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread
@@ -155,7 +155,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
all: $(OBJECTS) $(BINS) scriptToBin
-@@ -183,9 +180,6 @@ $(LEFTALIGN): $(SMITHWATERMAN)
+@@ -183,9 +180,6 @@
$(INDELALLELE): $(SMITHWATERMAN)
@@ -165,7 +165,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
#$(FSOM):
# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
-@@ -227,10 +221,8 @@ clean:
+@@ -227,10 +221,8 @@
rm -rf $(OBJ_DIR)
cd tabixpp && $(MAKE) clean
cd smithwaterman && $(MAKE) clean
=====================================
debian/patches/use_packaged_fermi-lite
=====================================
@@ -4,9 +4,9 @@ Description: Use the Debian package of fermi-lite
Adjust for the renamed bseq1_t→fml_seq1_t
See https://github.com/lh3/fermi-lite/issues/5
---- a/Makefile
-+++ b/Makefile
-@@ -211,7 +211,6 @@ GBWT_DIR:=deps/gbwt
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -211,7 +211,6 @@
GBWTGRAPH_DIR=deps/gbwtgraph
PROGRESS_BAR_DIR:=deps/progress_bar
FASTAHACK_DIR:=deps/fastahack
@@ -14,7 +14,7 @@ See https://github.com/lh3/fermi-lite/issues/5
HTSLIB_DIR:=deps/htslib
VCFLIB_DIR:=deps/vcflib
GSSW_DIR:=deps/gssw
-@@ -253,7 +252,6 @@ LIB_DEPS += $(LIB_DIR)/libgssw.a
+@@ -253,7 +252,6 @@
LIB_DEPS += $(LIB_DIR)/libvcfh.a
LIB_DEPS += $(LIB_DIR)/libsonlib.a
LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
@@ -22,7 +22,7 @@ See https://github.com/lh3/fermi-lite/issues/5
LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
LIB_DEPS += $(LIB_DIR)/libstructures.a
LIB_DEPS += $(LIB_DIR)/libvw.a
-@@ -516,9 +514,6 @@ $(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/lib
+@@ -500,9 +498,6 @@
$(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -c -o $@ $< $(FILTER)
@@ -32,9 +32,9 @@ See https://github.com/lh3/fermi-lite/issues/5
# 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/
---- a/src/srpe.cpp
-+++ b/src/srpe.cpp
-@@ -70,7 +70,7 @@ namespace vg{
+--- vg.orig/src/srpe.cpp
++++ vg/src/srpe.cpp
+@@ -70,7 +70,7 @@
}
@@ -43,7 +43,7 @@ See https://github.com/lh3/fermi-lite/issues/5
read->seq = (char*) a.sequence().c_str();
read->qual = (char*) a.quality().c_str();
read->l_seq = a.sequence().length();
-@@ -95,7 +95,7 @@ namespace vg{
+@@ -95,7 +95,7 @@
void SRPE::assemble(vector<Alignment> alns, vector<fml_utg_t>& unitigs){
int n_seqs, n_utgs;
n_seqs = alns.size();
@@ -52,9 +52,9 @@ See https://github.com/lh3/fermi-lite/issues/5
for (int i = 0; i < n_seqs; ++i){
aln_to_bseq( alns[i], mr_bseqs + i );
}
---- a/src/srpe.hpp
-+++ b/src/srpe.hpp
-@@ -155,7 +155,7 @@ public:
+--- vg.orig/src/srpe.hpp
++++ vg/src/srpe.hpp
+@@ -155,7 +155,7 @@
double discordance_score(vector<Alignment> alns, VG* subgraph);
// Convert Alignments to the read-like objects Fermi-lite uses in assembly
=====================================
debian/patches/use_packaged_jemalloc
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian packaged version of jemalloc
---- a/Makefile
-+++ b/Makefile
-@@ -207,7 +207,6 @@ CONFIGURATION_OBJ =
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -207,7 +207,6 @@
RAPTOR_DIR:=deps/raptor
@@ -10,7 +10,7 @@ Description: Use the Debian packaged version of jemalloc
LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
SDSL_DIR:=deps/sdsl-lite
SNAPPY_DIR:=deps/snappy
-@@ -311,7 +310,6 @@ LINK_DEPS =
+@@ -311,7 +310,6 @@
ifneq ($(shell uname -s),Darwin)
# Use jemalloc
@@ -18,7 +18,7 @@ Description: Use the Debian packaged version of jemalloc
LD_LIB_FLAGS += -ljemalloc
endif
-@@ -374,9 +372,6 @@ endif
+@@ -374,9 +372,6 @@
test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/json2pb.h $(SRC_DIR)/vg.hpp
. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp -lvg $(LD_LIB_FLAGS) $(ROCKSDB_LDFLAGS) $(FILTER)
@@ -28,3 +28,11 @@ Description: Use the Debian packaged version of jemalloc
# 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
+@@ -749,7 +744,6 @@
+ cd $(DEP_DIR) && cd gfakluge && $(MAKE) clean
+ cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
+ cd $(DEP_DIR) && cd structures && $(MAKE) clean
+- cd $(DEP_DIR) && cd jemalloc && $(MAKE) clean || true
+ cd $(DEP_DIR) && cd vowpal_wabbit && $(MAKE) clean
+ cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
+ cd $(DEP_DIR) && cd libhandlegraph && $(MAKE) clean
=====================================
debian/patches/use_packaged_libbackward-cpp
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian version of cpp-backward
---- a/Makefile
-+++ b/Makefile
-@@ -227,7 +227,6 @@ DYNAMIC_DIR:=deps/DYNAMIC
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -227,7 +227,6 @@
SSW_DIR:=deps/ssw/src
LINLS_DIR:=deps/sublinear-Li-Stephens
STRUCTURES_DIR:=deps/structures
@@ -10,7 +10,7 @@ Description: Use the Debian version of cpp-backward
DOZEU_DIR:=deps/dozeu
ELFUTILS_DIR:=deps/elfutils
VOWPALWABBIT_DIR:=deps/vowpal_wabbit
-@@ -297,7 +296,6 @@ DEPS += $(INC_DIR)/sparsepp/spp.h
+@@ -297,7 +296,6 @@
DEPS += $(INC_DIR)/gfakluge.hpp
DEPS += $(INC_DIR)/sha1.hpp
DEPS += $(INC_DIR)/progress_bar.hpp
@@ -18,7 +18,7 @@ Description: Use the Debian version of cpp-backward
DEPS += $(INC_DIR)/dozeu/dozeu.h
DEPS += $(INC_DIR)/mmmultimap.hpp
DEPS += $(INC_DIR)/ips4o.hpp
-@@ -549,9 +547,6 @@ $(LIB_DIR)/liballreduce.a: $(LIB_DIR)/li
+@@ -550,9 +548,6 @@
$(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hpp
+cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
=====================================
debian/patches/use_packaged_libdeflate
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian package for libdeflate
---- a/Makefile
-+++ b/Makefile
-@@ -36,7 +36,7 @@ INCLUDE_FLAGS:=-I$(CWD)/$(INC_DIR) -I. -
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -36,7 +36,7 @@
# Define libraries to link against. Make sure to always link statically against
# htslib and libdeflate and Protobuf so that we can use position-dependent code
# there for speed.
@@ -11,7 +11,7 @@ Description: Use the Debian package for libdeflate
# Use pkg-config to find Cairo and all the libs it uses
LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
-@@ -233,7 +233,6 @@ DOZEU_DIR:=deps/dozeu
+@@ -233,7 +233,6 @@
ELFUTILS_DIR:=deps/elfutils
BOOST_DIR:=deps/boost-subset
VOWPALWABBIT_DIR:=deps/vowpal_wabbit
@@ -19,7 +19,7 @@ Description: Use the Debian package for libdeflate
LIBVGIO_DIR:=deps/libvgio
LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
LIBBDSG_DIR:=deps/libbdsg
-@@ -275,7 +274,6 @@ LIB_DEPS += $(LIB_DIR)/libstructures.a
+@@ -275,7 +274,6 @@
LIB_DEPS += $(LIB_DIR)/libvw.a
LIB_DEPS += $(LIB_DIR)/liballreduce.a
LIB_DEPS += $(LIB_DIR)/libboost_program_options.a
@@ -27,7 +27,7 @@ Description: Use the Debian package for libdeflate
LIB_DEPS += $(LIB_DIR)/libvgio.a
LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
LIB_DEPS += $(LIB_DIR)/libbdsg.a
-@@ -459,28 +457,11 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLE
+@@ -459,28 +457,12 @@
+. ./source_me.sh && cd $(LIBHANDLEGRAPH_DIR) && cmake . && $(MAKE) $(FILTER) && cp libhandlegraph.a $(CWD)/$(LIB_DIR) && cp -r src/include/handlegraph $(CWD)/$(INC_DIR)
@@ -47,7 +47,7 @@ Description: Use the Debian package for libdeflate
- +. ./source_me.sh && cd $(LIBDEFLATE_DIR) && V=1 $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
-
-# We build htslib after libdeflate so it can use libdeflate
--# We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
+ # We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
# We also have to have the shared libdeflate or we will get complaints that the static one is not position independent.
# If we need either the library or the pkg-config file (which we didn't used to ship), run the whole build.
# We use a wildcard match to make sure make understands that both files come from one command run.
=====================================
debian/patches/use_packaged_libtsl-hopscotch-map-dev
=====================================
@@ -0,0 +1,59 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Use the tsl-hopscotch-map cmake target
+--- vg.orig/deps/DYNAMIC/CMakeLists.txt
++++ vg/deps/DYNAMIC/CMakeLists.txt
+@@ -14,23 +14,12 @@
+
+ include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)
+
+-# hopscotch_map
+-ExternalProject_Add(hopscotch_map
+- GIT_REPOSITORY "https://github.com/Tessil/hopscotch-map.git"
+- BUILD_IN_SOURCE TRUE
+- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR} # TODO ADD static build flag
+- UPDATE_COMMAND ""
+- INSTALL_COMMAND ""
+- BUILD_COMMAND ""
+- CONFIGURE_COMMAND "")
+-ExternalProject_Get_property(hopscotch_map INSTALL_DIR)
+-set(hopscotch_map_INCLUDE "${INSTALL_DIR}/src/hopscotch_map/include/")
++find_package(tsl-hopscotch-map REQUIRED)
+
+ include_directories(${PROJECT_SOURCE_DIR}/include)
+ include_directories(${PROJECT_SOURCE_DIR}/include/internal)
+ include_directories(${PROJECT_SOURCE_DIR}/include/algorithms)
+ include_directories(${PROJECT_SOURCE_DIR}/include/algorithms/cw-bwt)
+-include_directories(${INSTALL_DIR}/src/hopscotch_map/include)
+
+ message("Building in ${CMAKE_BUILD_TYPE} mode")
+
+@@ -54,11 +43,10 @@
+ add_executable(cw-bwt cw-bwt.cpp)
+ add_executable(benchmark benchmark.cpp)
+
+-add_dependencies(debug hopscotch_map)
+-add_dependencies(rle_lz77_v1 hopscotch_map)
+-add_dependencies(rle_lz77_v2 hopscotch_map)
+-add_dependencies(h0_lz77 hopscotch_map)
+-add_dependencies(rle_bwt hopscotch_map)
+-add_dependencies(cw-bwt hopscotch_map)
+-add_dependencies(benchmark hopscotch_map)
+-
++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)
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -431,7 +431,7 @@
+ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMIC_DIR)/include/*.hpp $(DYNAMIC_DIR)/include/internal/*.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 && cmake .. && make && cp -r hopscotch_map-prefix/src/hopscotch_map/include/* $(CWD)/$(INC_DIR)/
++ cd $(CWD)/$(DYNAMIC_DIR) && rm -Rf build && mkdir -p build && cd build && cmake .. && make
+ # 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/* $(INC_DIR)/dynamic
=====================================
debian/patches/use_packaged_protobuf
=====================================
@@ -0,0 +1,73 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Use the Debian packaged version of protobuf
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -35,7 +35,7 @@
+ # Define libraries to link against. Make sure to always link statically against
+ # htslib and libdeflate and Protobuf so that we can use position-dependent code
+ # there for speed.
+-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lhandlegraph -lvcflib -lgssw -lssw $(CWD)/$(LIB_DIR)/libprotobuf.a -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lgfakluge -lraptor2 -lsdsl -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg
++LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lhandlegraph -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lgfakluge -lraptor2 -lsdsl -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg
+ # Use pkg-config to find Cairo and all the libs it uses
+ LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
+
+@@ -173,7 +173,6 @@
+
+
+ RAPTOR_DIR:=deps/raptor
+-PROTOBUF_DIR:=deps/protobuf
+ LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
+ SDSL_DIR:=deps/sdsl-lite
+ SNAPPY_DIR:=deps/snappy
+@@ -211,7 +210,6 @@
+ # But that requires fancy ar scripting.
+ # If you just pass them to ar it puts the library *file* in libvg where nothing can read it.
+ LIB_DEPS =
+-LIB_DEPS += $(LIB_DIR)/libprotobuf.a
+ LIB_DEPS += $(LIB_DIR)/libsdsl.a
+ LIB_DEPS += $(LIB_DIR)/libssw.a
+ LIB_DEPS += $(LIB_DIR)/libsnappy.a
+@@ -291,13 +289,6 @@
+ ln -s `which shuf` $(BIN_DIR)/shuf
+ endif
+
+-# Make sure we have protoc built, and the protobuf lib
+-bin/protoc: $(LIB_DIR)/libprotobuf.a
+-$(LIB_DIR)/libprotobuf.a: deps/protobuf/src/google/protobuf/*.cc
+- rm -rf $(LIB_DIR)/libprotobuf* $(LIB_DIR)/libprotoc*
+- rm -Rf include/google/protobuf/
+- +. ./source_me.sh && cd $(PROTOBUF_DIR) && ./autogen.sh && export DIST_LANG=cpp && ./configure --prefix="$(CWD)" $(FILTER) && $(MAKE) $(FILTER) && $(MAKE) install && export PATH=$(CWD)/bin:$$PATH
+-
+ test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/json2pb.h $(SRC_DIR)/vg.hpp
+ . ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp -lvg $(LD_LIB_FLAGS) $(FILTER)
+
+@@ -347,7 +338,7 @@
+ # But we don't delete libvgio.dylib; Mac insists on it for some reason.
+ # We also need to clear out the old Protobuf header in case Protobuf updated;
+ # we don't want to accidentally build against it.
+-$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIB_DIR)/libprotobuf.a $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp
++$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp
+ +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 && cd $(LIBVGIO_DIR) && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_PREFIX_PATH=$(CWD) -DCMAKE_LIBRARY_PATH=$(CWD)/$(LIB_DIR) -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib . $(FILTER) && $(MAKE) clean && VERBOSE=1 $(MAKE) $(FILTER) && $(MAKE) install && rm -f $(CWD)/$(LIB_DIR)/libvgio.so
+@@ -579,7 +570,7 @@
+ $(RM) -r $(OBJ_DIR)/*.o $(OBJ_DIR)/*.d
+ $(RM) -f $(INC_DIR)/vg_git_version.hpp $(INC_DIR)/vg_system_version.hpp
+
+-clean: clean-protobuf clean-vcflib
++clean: clean-vcflib
+ $(RM) -r $(BIN_DIR)
+ $(RM) -r $(LIB_DIR)
+ $(RM) -r $(UNITTEST_OBJ_DIR)
+@@ -612,11 +603,6 @@
+ # lru_cache is never built because it is header-only.
+ # bash-tap is never built either.
+
+-clean-protobuf:
+- cd $(DEP_DIR) && cd protobuf && $(MAKE) clean
+- rm -f $(LIB_DIR)/libprotobuf.a
+- rm -rf $(INC_DIR)/google/protobuf/
+-
+ clean-vcflib:
+ cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
+ rm -f $(LIB_DIR)/libvcfh.a
=====================================
debian/patches/use_packaged_raptor2
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian package for raptor/rapper
---- a/Makefile
-+++ b/Makefile
-@@ -204,7 +204,6 @@ CONFIGURATION_OBJ =
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -204,7 +204,6 @@
@@ -10,7 +10,7 @@ Description: Use the Debian package for raptor/rapper
LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
SDSL_DIR:=deps/sdsl-lite
SNAPPY_DIR:=deps/snappy
-@@ -259,7 +258,6 @@ LIB_DEPS += $(LIB_DIR)/libgssw.a
+@@ -259,7 +258,6 @@
LIB_DEPS += $(LIB_DIR)/libvcfh.a
LIB_DEPS += $(LIB_DIR)/libsonlib.a
LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
@@ -18,7 +18,7 @@ Description: Use the Debian package for raptor/rapper
LIB_DEPS += $(LIB_DIR)/libfml.a
LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
LIB_DEPS += $(LIB_DIR)/libstructures.a
-@@ -285,7 +283,6 @@ DEPS += $(INC_DIR)/progress_bar.hpp
+@@ -285,7 +283,6 @@
DEPS += $(INC_DIR)/dozeu/dozeu.h
DEPS += $(INC_DIR)/mmmultimap.hpp
DEPS += $(INC_DIR)/ips4o.hpp
@@ -26,7 +26,7 @@ Description: Use the Debian package for raptor/rapper
DEPS += $(INC_DIR)/BooPHF.h
# Only depend on these files for the final linking stage.
-@@ -333,7 +330,7 @@ get-deps:
+@@ -333,7 +330,7 @@
# And we have submodule deps to build
deps: $(DEPS)
@@ -35,7 +35,7 @@ Description: Use the Debian package for raptor/rapper
. ./source_me.sh && cd test && prove -v t
docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp
-@@ -484,23 +481,6 @@ $(LIB_DIR)/libsonlib.a: $(CWD)/$(DEP_DIR
+@@ -485,23 +482,6 @@
$(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
@@ -59,7 +59,7 @@ Description: Use the Debian package for raptor/rapper
$(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)/
-@@ -722,7 +702,6 @@ clean: clean-vcflib
+@@ -705,7 +685,6 @@
cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
cd $(DEP_DIR) && cd libhandlegraph && $(MAKE) clean
cd $(DEP_DIR) && cd libvgio && $(MAKE) clean
=====================================
debian/patches/use_packaged_rocksdb
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian packaged version of rocksdb
---- a/Makefile
-+++ b/Makefile
-@@ -171,7 +171,6 @@ else
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -171,7 +171,6 @@
FILTER=
endif
@@ -10,7 +10,7 @@ Description: Use the Debian packaged version of rocksdb
# TODO: configure RPATH-equivalent on OS X for finding libraries without environment variables at runtime
# RocksDB's dependecies depend on whether certain compression libraries
-@@ -179,8 +178,7 @@ ROCKSDB_PORTABLE=PORTABLE=1 # needed to
+@@ -179,8 +178,7 @@
# detect these from its self-configuration. It has to be lazy because
# the configuration (make_config.mk) won't exist until after RocksDB
# is built by this Makefile.
@@ -20,7 +20,7 @@ Description: Use the Debian packaged version of rocksdb
# 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.
-@@ -210,7 +208,6 @@ RAPTOR_DIR:=deps/raptor
+@@ -210,7 +208,6 @@
LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
SDSL_DIR:=deps/sdsl-lite
SNAPPY_DIR:=deps/snappy
@@ -28,7 +28,7 @@ Description: Use the Debian packaged version of rocksdb
GCSA2_DIR:=deps/gcsa2
GBWT_DIR:=deps/gbwt
GBWTGRAPH_DIR=deps/gbwtgraph
-@@ -254,7 +251,6 @@ LIB_DEPS =
+@@ -254,7 +251,6 @@
LIB_DEPS += $(LIB_DIR)/libsdsl.a
LIB_DEPS += $(LIB_DIR)/libssw.a
LIB_DEPS += $(LIB_DIR)/libsnappy.a
@@ -36,7 +36,7 @@ Description: Use the Debian packaged version of rocksdb
LIB_DEPS += $(LIB_DIR)/libgcsa2.a
LIB_DEPS += $(LIB_DIR)/libgbwt.a
LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
-@@ -316,12 +312,12 @@ endif
+@@ -316,12 +312,12 @@
# For a normal dynamic build we remove the static build marker
$(BIN_DIR)/$(EXE): $(OBJ_DIR)/main.o $(LIB_DIR)/libvg.a $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) $(DEPS) $(LINK_DEPS)
-rm -f $(LIB_DIR)/vg_is_static
@@ -51,7 +51,7 @@ Description: Use the Debian packaged version of rocksdb
-touch $(LIB_DIR)/vg_is_static
# We don't want to always rebuild the static vg if no files have changed.
-@@ -368,7 +364,7 @@ else
+@@ -368,7 +364,7 @@
endif
test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/json2pb.h $(SRC_DIR)/vg.hpp
@@ -60,7 +60,7 @@ Description: Use the Debian packaged version of rocksdb
# 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.
-@@ -388,9 +384,6 @@ $(LIB_DIR)/libssw.a: $(SSW_DIR)/*.c $(SS
+@@ -388,9 +384,6 @@
$(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/
@@ -70,7 +70,7 @@ Description: Use the Debian packaged version of rocksdb
$(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)
-@@ -712,7 +705,7 @@ clean-vg:
+@@ -713,7 +706,7 @@
$(RM) -r $(OBJ_DIR)/*.o $(OBJ_DIR)/*.d
$(RM) -f $(INC_DIR)/vg_git_version.hpp $(INC_DIR)/vg_system_version.hpp
@@ -79,3 +79,15 @@ Description: Use the Debian packaged version of rocksdb
$(RM) -r $(BIN_DIR)
$(RM) -r $(LIB_DIR)
$(RM) -r $(UNITTEST_OBJ_DIR)
+@@ -747,11 +740,6 @@
+ # lru_cache is never built because it is header-only
+ # bash-tap is never built either
+
+-clean-rocksdb:
+- cd $(DEP_DIR) && cd rocksdb && $(MAKE) clean
+- rm -f $(LIB_DIR)/librocksdb.a
+- rm -rf $(INC_DIR)/rocksdb/
+-
+ clean-vcflib:
+ cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
+ rm -f $(LIB_DIR)/libvcfh.a
=====================================
debian/patches/use_packaged_smithwaterman
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: make the vcflib codecopy less bad by using the smithwaterman library
---- a/deps/vcflib/Makefile
-+++ b/deps/vcflib/Makefile
-@@ -119,11 +119,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
+--- vg.orig/deps/vcflib/Makefile
++++ vg/deps/vcflib/Makefile
+@@ -119,11 +119,6 @@
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
TABIX = tabixpp/tabix.o
@@ -14,7 +14,7 @@ Description: make the vcflib codecopy less bad by using the smithwaterman librar
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
-@@ -134,8 +129,8 @@ HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabix
+@@ -134,8 +129,8 @@
HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread
@@ -25,7 +25,7 @@ Description: make the vcflib codecopy less bad by using the smithwaterman librar
all: $(OBJECTS) $(BINS) scriptToBin
-@@ -155,7 +150,7 @@ profiling:
+@@ -155,7 +150,7 @@
gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS)" all
@@ -34,7 +34,7 @@ Description: make the vcflib codecopy less bad by using the smithwaterman librar
$(CXX) $(CPPFLAGS) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
# $(CXX) $(CPPFLAGS) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) -lvcflib $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-@@ -168,17 +163,6 @@ intervaltree: pre
+@@ -168,17 +163,6 @@
$(TABIX): pre
cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" HTS_HEADERS="" $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
@@ -52,7 +52,7 @@ Description: make the vcflib codecopy less bad by using the smithwaterman librar
#$(FSOM):
# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
-@@ -188,11 +172,11 @@ $(FILEVERCMP): pre
+@@ -188,11 +172,11 @@
$(SHORTBINS): pre
$(MAKE) bin/$@
@@ -67,7 +67,7 @@ Description: make the vcflib codecopy less bad by using the smithwaterman librar
cp libvcflib.a $(LIB_DIR)
-@@ -219,7 +203,6 @@ clean:
+@@ -219,7 +203,6 @@
rm -rf $(INC_DIR)
rm -rf $(OBJ_DIR)
cd tabixpp && $(MAKE) clean
@@ -75,9 +75,9 @@ Description: make the vcflib codecopy less bad by using the smithwaterman librar
cd multichoose && $(MAKE) clean
cd fsom && $(MAKE) clean
cd test && $(MAKE) clean
---- a/Makefile
-+++ b/Makefile
-@@ -31,12 +31,12 @@ include $(wildcard $(UNITTEST_OBJ_DIR)/*
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -31,12 +31,12 @@
CXXFLAGS := -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP $(CXXFLAGS)
# Set include flags. All -I options need to go in here, so the first directory listed is genuinely searched first.
@@ -87,8 +87,8 @@ Description: make the vcflib codecopy less bad by using the smithwaterman librar
# Define libraries to link against. Make sure to always link statically against
# htslib and libdeflate and Protobuf so that we can use position-dependent code
# there for speed.
--LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack)
-+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
+-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack)
++LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
# Use pkg-config to find Cairo and all the libs it uses
LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
=====================================
debian/patches/use_packaged_sparsehash
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian package for sparsehash
---- a/Makefile
-+++ b/Makefile
-@@ -215,7 +215,6 @@ FERMI_DIR:=deps/fermi-lite
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -215,7 +215,6 @@
HTSLIB_DIR:=deps/htslib
VCFLIB_DIR:=deps/vcflib
GSSW_DIR:=deps/gssw
@@ -10,7 +10,7 @@ Description: Use the Debian package for sparsehash
SPARSEPP_DIR:=deps/sparsepp
SHA1_DIR:=deps/sha1
DYNAMIC_DIR:=deps/DYNAMIC
-@@ -273,7 +272,6 @@ DEPS += $(INC_DIR)/gbwt/dynamic_gbwt.h
+@@ -273,7 +272,6 @@
DEPS += $(INC_DIR)/gbwtgraph/gbwtgraph.h
DEPS += $(INC_DIR)/lru_cache.h
DEPS += $(INC_DIR)/dynamic/dynamic.hpp
@@ -18,7 +18,7 @@ Description: Use the Debian package for sparsehash
DEPS += $(INC_DIR)/sparsepp/spp.h
DEPS += $(INC_DIR)/gfakluge.hpp
DEPS += $(INC_DIR)/sha1.hpp
-@@ -455,10 +453,7 @@ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMI
+@@ -456,10 +454,7 @@
# Otherwise we get dynamic.hpp without its deps
mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/* $(INC_DIR)/dynamic
@@ -30,7 +30,7 @@ Description: Use the Debian package for sparsehash
+cp -r $(SPARSEPP_DIR)/sparsepp $(INC_DIR)/
#$(INC_DIR)/Variant.h
-@@ -675,7 +670,6 @@ clean: clean-vcflib
+@@ -659,7 +654,6 @@
$(RM) -r $(INC_DIR)
$(RM) -r share/
cd $(DEP_DIR) && cd sonLib && $(MAKE) clean
=====================================
debian/patches/use_packaged_ssw
=====================================
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Use the Debian packaged version of libssw
---- a/Makefile
-+++ b/Makefile
-@@ -218,7 +218,6 @@ GSSW_DIR:=deps/gssw
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -218,7 +218,6 @@
SPARSEPP_DIR:=deps/sparsepp
SHA1_DIR:=deps/sha1
DYNAMIC_DIR:=deps/DYNAMIC
@@ -10,7 +10,7 @@ Description: Use the Debian packaged version of libssw
LINLS_DIR:=deps/sublinear-Li-Stephens
STRUCTURES_DIR:=deps/structures
DOZEU_DIR:=deps/dozeu
-@@ -245,7 +244,6 @@ DEP_OBJ += $(OBJ_DIR)/Fasta.o
+@@ -245,7 +244,6 @@
# If you just pass them to ar it puts the library *file* in libvg where nothing can read it.
LIB_DEPS =
LIB_DEPS += $(LIB_DIR)/libsdsl.a
@@ -18,7 +18,7 @@ Description: Use the Debian packaged version of libssw
LIB_DEPS += $(LIB_DIR)/libgcsa2.a
LIB_DEPS += $(LIB_DIR)/libgbwt.a
LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
-@@ -359,9 +357,6 @@ else
+@@ -359,9 +357,6 @@
+. ./source_me.sh && cd $(SDSL_DIR) && BUILD_PORTABLE=1 ./install.sh $(CWD) $(FILTER)
endif
@@ -28,7 +28,7 @@ Description: Use the Debian packaged version of libssw
$(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)
-@@ -676,7 +671,6 @@ clean: clean-vcflib
+@@ -660,7 +655,6 @@
cd $(DEP_DIR) && cd gbwt && $(MAKE) clean
cd $(DEP_DIR) && cd gbwtgraph && $(MAKE) clean
cd $(DEP_DIR) && cd gssw && $(MAKE) clean
@@ -36,9 +36,9 @@ Description: Use the Debian packaged version of libssw
cd $(DEP_DIR) && cd progress_bar && $(MAKE) clean
cd $(DEP_DIR) && cd sdsl-lite && ./uninstall.sh || true
cd $(DEP_DIR) && cd libVCFH && $(MAKE) clean
---- a/deps/vcflib/Makefile
-+++ b/deps/vcflib/Makefile
-@@ -151,11 +151,6 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
+--- vg.orig/deps/vcflib/Makefile
++++ vg/deps/vcflib/Makefile
+@@ -151,11 +151,6 @@
#CXXFLAGS = -O2
#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
@@ -50,7 +50,7 @@ Description: Use the Debian packaged version of libssw
openmp:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
-@@ -200,11 +195,11 @@ $(FILEVERCMP): pre
+@@ -200,11 +195,11 @@
$(SHORTBINS): pre
$(MAKE) bin/$@
@@ -65,7 +65,7 @@ Description: Use the Debian packaged version of libssw
cp libvcflib.a $(LIB_DIR)
-@@ -225,7 +220,6 @@ update: pull all
+@@ -225,7 +220,6 @@
clean:
rm -f $(BINS) $(OBJECTS)
@@ -73,8 +73,8 @@ Description: Use the Debian packaged version of libssw
rm -f libvcflib.a
rm -rf $(BIN_DIR)
rm -rf $(LIB_DIR)
---- a/deps/vcflib/src/Variant.h
-+++ b/deps/vcflib/src/Variant.h
+--- vg.orig/deps/vcflib/src/Variant.h
++++ vg/deps/vcflib/src/Variant.h
@@ -20,7 +20,7 @@
#include "tabix.hpp"
#include "SmithWatermanGotoh.h"
View it on GitLab: https://salsa.debian.org/med-team/vg/compare/48a9a4b78e2f27e24ae81cfd15adc55b61deb1ab...fa250714ac4354ff7c0c255c203aa13739dc5058
--
View it on GitLab: https://salsa.debian.org/med-team/vg/compare/48a9a4b78e2f27e24ae81cfd15adc55b61deb1ab...fa250714ac4354ff7c0c255c203aa13739dc5058
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