[med-svn] [Git][med-team/vg][master] 17 commits: Refresh use_packaged_vcflib

Étienne Mollier gitlab at salsa.debian.org
Wed Dec 16 21:13:04 GMT 2020 


Étienne Mollier pushed to branch master at Debian Med / vg


Commits:
eeabb8dd by Étienne Mollier at 2020-12-14T21:48:42+01:00
Refresh use_packaged_vcflib

- - - - -
5e88a8bd by Étienne Mollier at 2020-12-14T21:50:21+01:00
refresh use_packaged_libdeflate

- - - - -
b7c965a1 by Étienne Mollier at 2020-12-14T21:54:11+01:00
refresh use_packaged_htslib

- - - - -
4140bfe5 by Michael R. Crusoe at 2020-12-14T22:22:11+01:00
find Variant.h in /usr/include/vcflib

- - - - -
ccec324e by Michael R. Crusoe at 2020-12-14T22:27:49+01:00
update debian/clean

- - - - -
79113083 by Étienne Mollier at 2020-12-16T11:46:04+01:00
update changelog

- - - - -
f2506f30 by Étienne Mollier at 2020-12-16T17:04:54+01:00
d/control: ads build time test dependencies

In addition to the existing toolset, the test suite executes the
programs bgzip, from tabix, and xxd, so adding them as build time
dependencies.

- - - - -
d2b9c586 by Étienne Mollier at 2020-12-16T17:08:21+01:00
d/rules: fix calls to vg SIMDe variants

Probably due to being located in the wrong path, only the first
variant caught by the script was tested.  This rewrap also makes sure
the script uses absolute paths as much as possible, and does not
change working directory too much.

- - - - -
8af10a42 by Étienne Mollier at 2020-12-16T18:40:23+01:00
update changelog

- - - - -
c67c08fd by Étienne Mollier at 2020-12-16T19:11:21+01:00
d/rules: disable AVX variant as one test fails

- - - - -
fae5d0c4 by Étienne Mollier at 2020-12-16T19:34:59+01:00
updated false positives of typos

- - - - -
97a54eed by Étienne Mollier at 2020-12-16T19:35:27+01:00
fixed new typo in binaries

- - - - -
3b4f5c25 by Étienne Mollier at 2020-12-16T20:37:56+01:00
provided a "whatis" description to vg manual

- - - - -
4ce6bfbb by Étienne Mollier at 2020-12-16T20:49:18+01:00
d/rules: abort test if vg-plain fails

Other variants may not be capable of executing on the buildd, so
it is better to let them pass in a first time, or check for CPU
extensions available on the buildd on a second time.

- - - - -
7877c47e by Étienne Mollier at 2020-12-16T21:10:28+01:00
d/copyright: reorder spp_timer.h

The initial possition in the copyright file triggered a lintian
warning globbing-patterns-out-of-order.

- - - - -
4e6ad9e3 by Étienne Mollier at 2020-12-16T21:11:42+01:00
Make sure the libbz2 is dynamically linked.

- - - - -
1577a2a0 by Étienne Mollier at 2020-12-16T22:12:19+01:00
updated changelog

- - - - -


11 changed files:

- debian/changelog
- debian/clean
- debian/control
- debian/copyright
- debian/patches/spelling
- debian/patches/static
- debian/patches/use_packaged_htslib
- debian/patches/use_packaged_libdeflate
- debian/patches/use_packaged_vcflib
- debian/rules
- debian/vg.lintian-overrides


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,28 @@
 vg (1.29.0+ds-1) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Team upload.
   * New upstream version
   * Standards-Version: 4.5.1 (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Sat, 12 Dec 2020 06:33:05 +0100
+  [ Michael R. Crusoe ]
+  * find Variant.h in /usr/include/vcflib
+  * update debian/clean
+
+  [ Étienne Mollier ]
+  * refresh patches
+  * d/control: add build time test dependencies on tabix and xxd.
+  * d/rules: reviewed calls to vg-* SIMDe variants during build time tests.
+  * d/rules: disable AVX variant as one test fails
+  * d/rules: abort test if vg-plain fails
+  * lintian overrides: updated false positives of typos
+  * spelling patch: fixed a new typo in binaries
+  * provided a "whatis" description to vg manual
+  * d/copyright: reorder spp_timer.h to make sure globbing maps to the proper
+    license term for sparsepp, per lintian warning
+  * make sure the libbz2 is dynamically linked
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  Wed, 16 Dec 2020 22:06:06 +0100
 
 vg (1.27.1+ds-1) unstable; urgency=medium
 


=====================================
debian/clean
=====================================
@@ -2,8 +2,13 @@ deps/vowpal_wabbit/vowpalwabbit/.libs/
 deps/DYNAMIC/build/*
 deps/gssw/bin/
 deps/gssw/obj/
+deps/gbwt/*.d
+deps/gbwtgraph/*.d
+deps/gcsa2/*.d
 deps/libhandlegraph/CMakeFiles/
 obj/
+deps/libbdsg/bdsg/obj/
+deps/libbdsg/lib/*.a
 deps/libhandlegraph/*.a
 deps/libhandlegraph/*.so
 deps/sonLib/externalTools/quicktree_1.1/bin/*
@@ -33,3 +38,26 @@ deps/vowpal_wabbit/libtool
 deps/vowpal_wabbit/libvw.pc
 deps/vowpal_wabbit/vowpalwabbit/config.h
 deps/vowpal_wabbit/vowpalwabbit/stamp-h1
+include/xg.hpp
+include/vowpalwabbit/
+include/vg/
+include/tinyfa.hpp
+include/sublinearLS/
+include/structures/
+include/ssw_cpp.h
+include/sparsepp/
+include/sonLib/
+include/simde/
+include/ips4o.hpp
+include/ips4o/
+include/kseq.h
+include/kseq.h
+include/lru_cache.h
+include/mmmultimap.hpp
+include/mmmultiset.hpp
+include/pliib.hpp
+include/progress_bar.hpp
+include/sha1.hpp
+include/handlegraph/
+include/gssw.h
+


=====================================
debian/control
=====================================
@@ -50,6 +50,8 @@ Build-Depends: debhelper-compat (= 13),
                libfml-dev,
                libfastahack-dev,
                fastahack <!nocheck>,
+               tabix <!nocheck>,
+               xxd <!nocheck>,
                libsmithwaterman-dev,
                libdivsufsort-dev,
                libtsl-hopscotch-map-dev,


=====================================
debian/copyright
=====================================
@@ -35,7 +35,6 @@ Files-Excluded: deps/libdeflate
                 deps/htslib
 
 Files: *
-       deps/sparsepp/sparsepp/spp_timer.h
 Copyright: © 2014, 2010, 2012, 2014-2015 Erik Garrison
            2013, Pavel Shramov <shramov at mexmat.net>
            (C) 2009-2014, 2018 by Benedict Paten (benedictpaten at gmail.com)
@@ -96,6 +95,10 @@ Copyright: 2008-2018, Genome Research Ltd.
            (c) 2012 - ariel faigon for vowpal-wabbit
 License: BSD-3-clause
 
+Files: deps/sparsepp/sparsepp/spp_timer.h
+Copyright: 2016, Mariano Gonzalez
+License: MIT
+
 Files: deps/sonLib/sonLib_daemonize.py
 Copyright: (C) 2006-2012 by Glenn Hickey
            (C) 2005 Chad J. Schroeder


=====================================
debian/patches/spelling
=====================================
@@ -1,9 +1,9 @@
 From: Michael R. Crusoe <crusoe at debian.org>
 Subject: fix spelling typos
 Forwarded: https://github.com/vgteam/vg/pull/2863
---- 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*/)
    {
@@ -12,9 +12,9 @@ Forwarded: https://github.com/vgteam/vg/pull/2863
  
      // 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
@@ -23,9 +23,9 @@ Forwarded: https://github.com/vgteam/vg/pull/2863
        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/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:
@@ -34,3 +34,14 @@ Forwarded: https://github.com/vgteam/vg/pull/2863
      cerr.write(s.begin, s.end - s.begin);
      cerr << "'?\n";
    }
+--- vg.orig/src/unittest/genotypekit.cpp
++++ vg/src/unittest/genotypekit.cpp
+@@ -684,7 +684,7 @@
+     REQUIRE(finder->find_snarls().num_snarls() == 2);
+ }
+ 
+-TEST_CASE("IntegratedSnarlFinder safely handles a single node conencted component in a larger graph", "[genotype][integrated-snarl-finder]") {
++TEST_CASE("IntegratedSnarlFinder safely handles a single node connected component in a larger graph", "[genotype][integrated-snarl-finder]") {
+     
+     // Build a toy graph
+     const string graph_json = R"(


=====================================
debian/patches/static
=====================================
@@ -1,9 +1,9 @@
 Author: Michael R. Crusoe <crusoe at debian.org>
 Description: For Debian, don't statically link to cairo, jansson, libstdc++, libgcc
 Forwarded: not-needed
---- a/Makefile
-+++ b/Makefile
-@@ -52,7 +52,7 @@ INCLUDE_FLAGS :=$(shell pkg-config --cfl
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -52,14 +52,14 @@
  
  # Define libraries to link against.
  LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
@@ -12,7 +12,16 @@ Forwarded: not-needed
  # We omit Boost Program Options for now; we find it in a platform-dependent way.
  # By default it has no suffix
  BOOST_SUFFIX=""
-@@ -221,7 +221,7 @@ LD_LIB_FLAGS += -lrocksdb -lbz2
+ # We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code.
+-LD_STATIC_LIB_FLAGS := $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -lbz2 -llzma
++LD_STATIC_LIB_FLAGS := $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -llzma
+ # Some of our static libraries depend on libraries that may not always be avilable in static form.
+-LD_STATIC_LIB_DEPS := -lpthread -lm
++LD_STATIC_LIB_DEPS := -lpthread -lm -lbz2
+ # Use pkg-config to find dependencies.
+ # Always use --static so that we have the -l flags for transitive dependencies, in case we're doing a full static build.
+ # But only force static linking of the dependencies we want to use non-PIC code for, for speed.
+@@ -221,7 +221,7 @@
  # 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_htslib
=====================================
@@ -1,9 +1,9 @@
 Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Use the Debian package of htslib
 Forwarded: not-needed
---- a/Makefile
-+++ b/Makefile
-@@ -52,7 +52,7 @@ INCLUDE_FLAGS :=$(shell pkg-config --cfl
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -52,12 +52,12 @@
  
  # Define libraries to link against.
  LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
@@ -12,7 +12,13 @@ Forwarded: not-needed
  # We omit Boost Program Options for now; we find it in a platform-dependent way.
  # By default it has no suffix
  BOOST_SUFFIX=""
-@@ -174,9 +174,6 @@ else
+ # We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code.
+-LD_STATIC_LIB_FLAGS := $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -llzma
++LD_STATIC_LIB_FLAGS := -lhts -ldeflate -lz -llzma
+ # Some of our static libraries depend on libraries that may not always be avilable in static form.
+ LD_STATIC_LIB_DEPS := -lpthread -lm -lbz2
+ # Use pkg-config to find dependencies.
+@@ -174,9 +174,6 @@
      # We get OpenMP the normal way, using whatever the compiler knows about
      CXXFLAGS += -fopenmp
  
@@ -22,7 +28,7 @@ Forwarded: not-needed
      # Note shared libraries are so files
      SHARED_SUFFIX = so
      # Define options to start static linking of libraries on GNU ld.
-@@ -248,7 +245,6 @@ GCSA2_DIR:=deps/gcsa2
+@@ -248,7 +245,6 @@
  GBWT_DIR:=deps/gbwt
  GBWTGRAPH_DIR=deps/gbwtgraph
  PROGRESS_BAR_DIR:=deps/progress_bar
@@ -30,7 +36,7 @@ Forwarded: not-needed
  GSSW_DIR:=deps/gssw
  SPARSEPP_DIR:=deps/sparsepp
  SHA1_DIR:=deps/sha1
-@@ -281,7 +277,6 @@ LIB_DEPS += $(LIB_DIR)/libsdsl.a
+@@ -281,7 +277,6 @@
  LIB_DEPS += $(LIB_DIR)/libgcsa2.a
  LIB_DEPS += $(LIB_DIR)/libgbwt.a
  LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
@@ -38,7 +44,7 @@ Forwarded: not-needed
  LIB_DEPS += $(LIB_DIR)/libgssw.a
  LIB_DEPS += $(LIB_DIR)/libsonlib.a
  LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
-@@ -438,7 +433,7 @@ $(LIB_DIR)/cleaned_old_boost: $(wildcard
+@@ -438,7 +433,7 @@
  	+rm -Rf $(INC_DIR)/boost
  	+touch $(LIB_DIR)/cleaned_old_boost
  
@@ -47,7 +53,7 @@ Forwarded: not-needed
  	+rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h
  	+rm -Rf $(CWD)/$(INC_DIR)/vg/io/
  	+. ./source_me.sh && export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && cd $(LIBVGIO_DIR) && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_VERBOSE_MAKEFILE=ON -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 
-@@ -462,19 +457,6 @@ endif
+@@ -462,19 +457,6 @@
  $(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDEFLATE_DIR)/lib/*/*.h $(LIBDEFLATE_DIR)/lib/*.c $(LIBDEFLATE_DIR)/lib/*/*.c
  	+. ./source_me.sh && cd $(LIBDEFLATE_DIR) && V=1 $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
  
@@ -67,7 +73,7 @@ Forwarded: not-needed
  $(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)
  
-@@ -543,7 +525,7 @@ $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp
+@@ -543,7 +525,7 @@
  	+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
  
  # We don't need to hack the build to point at our htslib because sublinearLS gets its htslib from the include flags we set


=====================================
debian/patches/use_packaged_libdeflate
=====================================
@@ -1,9 +1,18 @@
 Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Use the Debian package for libdeflate
 Forwarded: not-needed
---- a/Makefile
-+++ b/Makefile
-@@ -272,7 +272,6 @@ BACKWARD_CPP_DIR:=deps/backward-cpp
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -57,7 +57,7 @@
+ # By default it has no suffix
+ BOOST_SUFFIX=""
+ # We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code.
+-LD_STATIC_LIB_FLAGS := $(CWD)/$(LIB_DIR)/libhts.a $(CWD)/$(LIB_DIR)/libdeflate.a -lz -lbz2 -llzma
++LD_STATIC_LIB_FLAGS := $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -lbz2 -llzma
+ # Some of our static libraries depend on libraries that may not always be avilable in static form.
+ LD_STATIC_LIB_DEPS := -lpthread -lm
+ # Use pkg-config to find dependencies.
+@@ -272,7 +272,6 @@
  DOZEU_DIR:=deps/dozeu
  ELFUTILS_DIR:=deps/elfutils
  VOWPALWABBIT_DIR:=deps/vowpal_wabbit
@@ -11,7 +20,7 @@ Forwarded: not-needed
  LIBVGIO_DIR:=deps/libvgio
  LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
  LIBBDSG_DIR:=deps/libbdsg
-@@ -313,7 +312,7 @@ LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
+@@ -313,7 +312,7 @@
  LIB_DEPS += $(LIB_DIR)/libstructures.a
  LIB_DEPS += $(LIB_DIR)/libvw.a
  LIB_DEPS += $(LIB_DIR)/liballreduce.a


=====================================
debian/patches/use_packaged_vcflib
=====================================
@@ -1,9 +1,9 @@
 Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Attempt to use the Debian version of vcflib
 Forwarded: not-needed
---- a/Makefile
-+++ b/Makefile
-@@ -48,11 +48,11 @@ DEPGEN_FLAGS := -MMD -MP
+--- vg.orig/Makefile
++++ vg/Makefile
+@@ -48,11 +48,11 @@
  # necessary on all platforms and suppresses warnings.
  # Also, pkg-config flags need to be made -isystem if our dependency install
  # directory is, or they might put a system HTSlib before ours.
@@ -17,7 +17,7 @@ Forwarded: not-needed
  # We omit Boost Program Options for now; we find it in a platform-dependent way.
  # By default it has no suffix
  BOOST_SUFFIX=""
-@@ -248,7 +248,6 @@ GCSA2_DIR:=deps/gcsa2
+@@ -248,7 +248,6 @@
  GBWT_DIR:=deps/gbwt
  GBWTGRAPH_DIR=deps/gbwtgraph
  PROGRESS_BAR_DIR:=deps/progress_bar
@@ -25,7 +25,7 @@ Forwarded: not-needed
  HTSLIB_DIR:=$(VCFLIB_DIR)/tabixpp/htslib
  GSSW_DIR:=deps/gssw
  SPARSEPP_DIR:=deps/sparsepp
-@@ -283,7 +282,6 @@ LIB_DEPS += $(LIB_DIR)/libgcsa2.a
+@@ -283,7 +282,6 @@
  LIB_DEPS += $(LIB_DIR)/libgbwt.a
  LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
  LIB_DEPS += $(LIB_DIR)/libhts.a
@@ -33,7 +33,7 @@ Forwarded: not-needed
  LIB_DEPS += $(LIB_DIR)/libgssw.a
  LIB_DEPS += $(LIB_DIR)/libsonlib.a
  LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
-@@ -357,7 +355,7 @@ get-deps:
+@@ -357,7 +355,7 @@
  # And we have submodule deps to build
  deps: $(DEPS)
  
@@ -42,7 +42,7 @@ Forwarded: not-needed
  	. ./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
-@@ -477,13 +475,6 @@ $(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DI
+@@ -477,13 +475,6 @@
  $(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(LIB_DIR)/libdeflate.a $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
  	+. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -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 && ls $(CWD)/$(INC_DIR)/htslib
  
@@ -56,7 +56,7 @@ Forwarded: not-needed
  $(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)
  
-@@ -712,7 +703,7 @@ clean-vg:
+@@ -712,7 +703,7 @@
  	$(RM) -r $(OBJ_DIR)/*.o $(OBJ_DIR)/*.d
  	$(RM) -f $(INC_DIR)/vg_system_version.hpp
  
@@ -65,7 +65,7 @@ Forwarded: not-needed
  	$(RM) -r $(BIN_DIR)
  	$(RM) -r $(LIB_DIR)
  	$(RM) -r $(UNITTEST_OBJ_DIR)
-@@ -728,7 +719,6 @@ clean: clean-vcflib
+@@ -728,7 +719,6 @@
  	cd $(DEP_DIR) && cd gssw && $(MAKE) clean
  	cd $(DEP_DIR) && cd progress_bar && $(MAKE) clean
  	cd $(DEP_DIR) && cd sdsl-lite && ./uninstall.sh || true
@@ -73,16 +73,21 @@ Forwarded: not-needed
  	cd $(DEP_DIR) && cd gfakluge && $(MAKE) clean
  	cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
  	cd $(DEP_DIR) && cd structures && $(MAKE) clean
-@@ -739,6 +729,3 @@ clean: clean-vcflib
+@@ -739,6 +729,3 @@
  	# lru_cache is never built because it is header-only
  	# bash-tap is never built either
  
 -clean-vcflib:
 -	cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
 -	cd $(INC_DIR) && rm -f BedReader.h convert.h join.h mt19937ar.h split.h Variant.h vec128int.h veclib_types.h
---- a/src/srpe.hpp
-+++ b/src/srpe.hpp
-@@ -6,7 +6,7 @@
+--- vg.orig/src/srpe.hpp
++++ vg/src/srpe.hpp
+@@ -2,11 +2,11 @@
+ #define VG_SRPE
+ #include <string>
+ #include <cstdint>
+-#include <Variant.h>
++#include <vcflib/Variant.h>
  #include "filter.hpp"
  #include "index.hpp"
  #include "path_index.hpp"
@@ -91,19 +96,22 @@ Forwarded: not-needed
  #include <vg/vg.pb.h>
  #include "fml.h"
  #include "vg.hpp"
---- a/src/subcommand/srpe_main.cpp
-+++ b/src/subcommand/srpe_main.cpp
-@@ -26,7 +26,7 @@
+--- vg.orig/src/subcommand/srpe_main.cpp
++++ vg/src/subcommand/srpe_main.cpp
+@@ -24,9 +24,9 @@
+ 
+ // TODO: Where even are these?
  #include <vg/vg.pb.h>
- #include "Variant.h"
+-#include "Variant.h"
++#include <vcflib/Variant.h>
  #include "Fasta.h"
 -#include "IntervalTree.h"
 +#include <intervaltree/IntervalTree.h>
  
  using namespace std;
  using namespace vg;
---- a/test/Makefile
-+++ b/test/Makefile
+--- vg.orig/test/Makefile
++++ vg/test/Makefile
 @@ -3,19 +3,11 @@
  CXX:=g++
  CXXFLAGS:=-O3 -std=c++11 -fopenmp -g
@@ -125,9 +133,9 @@ Forwarded: not-needed
  build_graph: build_graph.cpp
  	cd .. && . ./source_me.sh && $(MAKE) test/build_graph
  
---- a/test/t/02_vg_construct.t
-+++ b/test/t/02_vg_construct.t
-@@ -76,7 +76,7 @@ rm -f fail.vg
+--- vg.orig/test/t/02_vg_construct.t
++++ vg/test/t/02_vg_construct.t
+@@ -76,7 +76,7 @@
  # check that we produce a full graph
  
  refbp=$(fastahack -r x small/x.fa | tr -d '\n' | wc -c)
@@ -136,3 +144,80 @@ Forwarded: not-needed
      | cut -f 5,4 | tail -n+2 \
      | awk '{ x=length($2)-length($1); if (x > 0) { print x; } else if (x == 0) { print length($2); } }' \
          | awk '{ sum += $1 } END { print sum }')
+--- vg.orig/src/readfilter.hpp
++++ vg/src/readfilter.hpp
+@@ -11,7 +11,7 @@
+ 
+ #include "vg.hpp"
+ #include "handle.hpp"
+-#include "IntervalTree.h"
++#include <intervaltree/IntervalTree.h>
+ #include "annotation.hpp"
+ #include "multipath_alignment_emitter.hpp"
+ #include <vg/io/alignment_emitter.hpp>
+--- vg.orig/src/aligner.hpp
++++ vg/src/aligner.hpp
+@@ -11,7 +11,7 @@
+ #include "gssw.h"
+ #include <vg/vg.pb.h>
+ #include "vg.hpp"
+-#include "Variant.h"
++#include <vcflib/Variant.h>
+ #include "Fasta.h"
+ #include "path.hpp"
+ #include "utility.hpp"
+--- vg.orig/src/constructor.hpp
++++ vg/src/constructor.hpp
+@@ -22,7 +22,7 @@
+ #include <vg/vg.pb.h>
+ 
+ // We need vcflib
+-#include <Variant.h>
++#include <vcflib/Variant.h>
+ // And fastahack
+ #include <Fasta.h>
+ 
+--- vg.orig/src/deconstructor.hpp
++++ vg/src/deconstructor.hpp
+@@ -5,7 +5,7 @@
+ #include <ostream>
+ #include <sstream>
+ #include "genotypekit.hpp"
+-#include "Variant.h"
++#include <vcflib/Variant.h>
+ #include "handle.hpp"
+ #include "genotypekit.hpp"
+ #include "traversal_finder.hpp"
+--- vg.orig/src/utility.hpp
++++ vg/src/utility.hpp
+@@ -19,7 +19,7 @@
+ #include <vg/vg.pb.h>
+ #include "types.hpp"
+ #include "sha1.hpp"
+-#include "Variant.h"
++#include <vcflib/Variant.h>
+ 
+ namespace vg {
+ 
+--- vg.orig/src/vcf_buffer.hpp
++++ vg/src/vcf_buffer.hpp
+@@ -10,7 +10,7 @@
+ #include <tuple>
+ 
+ // We need vcflib
+-#include "Variant.h"
++#include <vcflib/Variant.h>
+ 
+ 
+ namespace vg {
+--- vg.orig/src/vg.hpp
++++ vg/src/vg.hpp
+@@ -33,7 +33,7 @@
+ #include "progressive.hpp"
+ #include "lru_cache.h"
+ 
+-#include "Variant.h"
++#include <vcflib/Variant.h>
+ #include "Fasta.h"
+ 
+ #include "swap_remove.hpp"


=====================================
debian/rules
=====================================
@@ -15,6 +15,30 @@ export CXXFLAGS=$(shell dpkg-buildflags --get CXXFLAGS)
 prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr
 libexecdir=$(prefix)/lib/$(DEB_SOURCE)
 
+# FIXME: avx excluded for 1.29.0+ds-1, the variant fails unit testing with:
+#	t/28_translate.t ......
+#	1..2
+#	not ok 1 - alignments used to modify a graph may be projected back to the original graph and used
+#	to regenerate the same graph
+#	#          got: '7899a03d71d6de1a0304aa9b95625fac'
+#	#     expected: 'ab1eb433cec6b150e5c08f273578c5d4'
+#	ok 2 - translation overlay works and produces a sane result
+#	Failed 1/2 subtests
+#	Statistics:
+#	Number of Non-Degenerate Snarls: 4
+#	Snarls traversed by reads: 4
+#	Snarls on reference: 0
+#	Snarl length distribution:
+#	Statistics:
+#	Number of Non-Degenerate Snarls: 4
+#	Snarls traversed by reads: 4
+#	Snarls on reference: 0
+#	Snarl length distribution:
+# (this was seen on Ryzen 5 3600, maybe it will differ on other models)
+AMD64_SIMDE=avx2 sse4.1 ssse3 sse3
+#AMD64_SIMDE=avx2 avx sse4.1 ssse3 sse3
+I386_SIMDE=sse2 sse
+
 %:
 	dh $@
 
@@ -34,7 +58,7 @@ override_dh_auto_build-arch:
 ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
 	mkdir -p $(prefix)
 	mkdir -p $(libexecdir)
-	for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \
+	for SIMD in $(AMD64_SIMDE) ; do \
 		export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \
 		make clean ; \
 		dh_auto_build -- SFX=-$${SIMD} all test/build_graph bin/shuf ; \
@@ -42,7 +66,7 @@ ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
 	CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" dh_auto_build -- SFX=-plain all test/build_graph bin/shuf
 	cp bin/vg-plain debian/help/vg
 ifeq (i386,$(DEB_HOST_ARCH))
-	for SIMD in sse2 sse ; do \
+	for SIMD in $(I386_SIMDE) ; do \
 		export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \
 		make clean ; \
 		dh_auto_build -- SFX=-$${SIMD} ; \
@@ -53,18 +77,37 @@ else
 	cp bin/vg debian/help/
 endif
 ifeq (,$(filter nodoc,$(DEB_BUILD_PROFILES)))
-	PATH=$$PATH:$(CURDIR)/debian/help help2man --no-discard-stderr --no-info --help-option=help --version-option=version vg > debian/vg.1
+	PATH=$$PATH:$(CURDIR)/debian/help \
+	help2man \
+		--no-discard-stderr \
+		--no-info \
+		--help-option=help \
+		--version-option=version \
+		--name='tools for working with genome variation graphs' \
+		vg > debian/vg.1
 endif
 
 override_dh_auto_test-arch:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
-	set +e ; for BIN in bin/vg-* ; do \
-	  echo Testing $${BIN} && cp $${BIN} debian/help/vg && \
-	  export PATH=$$PATH:$(CURDIR)/debian/help && . ./source_me.sh && cd test && prove -v t && cd .. ; \
-	done ; set -e
+	cp -v $(CURDIR)/bin/vg-* $(CURDIR)/debian/help/
+	set +e							\
+	; export PATH="$$PATH:$(CURDIR)/debian/help"		\
+	; for BIN in $(CURDIR)/debian/help/vg-*			\
+	; do	echo "Testing $${BIN}"				\
+		&& cp -v "$${BIN}" "$(CURDIR)/debian/help/vg"	\
+		&& . $(CURDIR)/source_me.sh			\
+		&& ( cd $(CURDIR)/test && prove -v t/ )		\
+		; if [ $$? != 0 ]				\
+		     && [ "$${BIN}" = "$(CURDIR)/debian/help/vg-plain" ] \
+		; then exit 255					\
+		; fi						\
+	; done							\
+	; set -e
 else
-	export PATH=$$PATH:$(CURDIR)/debian/help && . ./source_me.sh && cd test && prove -v t
+	export PATH=$$PATH:$(CURDIR)/debian/help	\
+	&& . $(CURDIR)/source_me.sh			\
+	&& ( cd $(CURDIR)/test && prove -v t/ )
 endif
 endif
 


=====================================
debian/vg.lintian-overrides
=====================================
@@ -1,4 +1,6 @@
 # false positive
-vg: spelling-error-in-binary bin/vg lengH length
-vg: spelling-error-in-binary bin/vg wiThe with
-
+vg: spelling-error-in-binary usr/lib/vg/vg-* boun bound
+vg: spelling-error-in-binary usr/lib/vg/vg-* defaulH default
+vg: spelling-error-in-binary usr/lib/vg/vg-* lengH length
+vg: spelling-error-in-binary usr/lib/vg/vg-* perfec perfect
+vg: spelling-error-in-binary usr/lib/vg/vg-* wiThe with



View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/e88e8a43e3be987ed3e5fb8ed0adce84d7fe8fa3...1577a2a0f698b5ec0948ca0a3a2fcfcb10e5bf82

-- 
View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/e88e8a43e3be987ed3e5fb8ed0adce84d7fe8fa3...1577a2a0f698b5ec0948ca0a3a2fcfcb10e5bf82
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