Merge pull request #3810 from vgteam/lr-giraffe

Long Read Giraffe Refactor
vgteam · Dec 14, 2022 · e31af2b · e31af2b · adamnovak · Dec 14, 2022
2 parents 9bc52ad + b9bf9a8
commit e31af2b
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Showing 35 changed files with 7,141 additions and 3,675 deletions.
diff --git a/.github/workflows/testmac.yml b/.github/workflows/testmac.yml
@@ -56,5 +56,15 @@ jobs:
         run: |
           export VG_FULL_TRACEBACK=1
           echo "Build with $(nproc) threads"
+          set +e
           make -j$(nproc) test
+          RETVAL=$?
+          set -e
+          # Whether vg testing succeeds or fails, see if we can get any Apple crash logs for it.
+          ls ~/Library/Logs/DiagnosticReports/
+          for CRASH_FILE in $(ls ~/Library/Logs/DiagnosticReports/vg-* 2>/dev/null) ; do
+              echo "vg crash report found: ${CRASH_FILE}"
+              cat ${CRASH_FILE}
+          done
+          exit $RETVAL
         shell: bash
diff --git a/Makefile b/Makefile
@@ -508,7 +508,7 @@ else
 endif
 
 test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/vg.hpp
-	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp $(LDFLAGS) -lvg $(LD_LIB_DIR_FLAGS) $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(FILTER)
+	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp $(LDFLAGS) $(LIB_DIR)/libvg.a $(LD_LIB_DIR_FLAGS) $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(FILTER)
 
 $(LIB_DIR)/libjemalloc.a: $(JEMALLOC_DIR)/src/*.c
 	+. ./source_me.sh && rm -Rf $(CWD)/$(INC_DIR)/jemalloc && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --disable-libdl --prefix=`pwd` $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && cp -r lib/* $(CWD)/$(LIB_DIR)/ && cp -r include/* $(CWD)/$(INC_DIR)/

diff --git a/deps/libhandlegraph b/deps/libhandlegraph
diff --git a/src/algorithms/chain_items.cpp b/src/algorithms/chain_items.cpp
+60 −24		src/dijkstra.cpp
+9 −2		src/include/handlegraph/algorithms/dijkstra.hpp