release 1.3.0-14-ga43013f4

Illumina · May 4, 2022 · 2e0ec68 · 2e0ec68
1 parent c87d93a
commit 2e0ec68
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Showing 106 changed files with 5,665 additions and 4,722 deletions.
diff --git a/INSTALL b/INSTALL
@@ -2,7 +2,7 @@ Prerequisites
 -------------
 
 * CentOS Linux release = 7.6.1810
-* gcc-c++ >= 4.8.5-36.el7_6.2
+* gcc-c++ >= 7.1
 * boost169-devel >= 1.69.0-1.el7
 * imake >= 1:3.82-23.el7
 

diff --git a/Makefile b/Makefile
@@ -19,16 +19,23 @@
 
 include config.mk
 
-all: $(programs:%=$(BUILD)/%)
+all: $(programs:%=$(DRAGEN_OS_BUILD)/%)
 
 .PHONY: clean
 clean:
 	$(RMDIR) $(DRAGEN_OS_BUILD_DIR_BASE)
 
 .PHONY: help
-clean:
 help: $(DRAGEN_OS_ROOT_DIR)/README.md
 	cat $<
+
+.PHONY: help-targets
+help-targets:
+	@$(ECHO) 'Default:   all'
+	@$(ECHO) 'Help:      help help-targets'
+	@$(ECHO) 'Cleanup:   clean'
+	@$(ECHO) 'Install:   install'
+	@$(ECHO) 'Libraries: $(library_targets)'
 
 ############################################################
 ##
@@ -50,7 +57,7 @@ POSTCOMPILE ?= mv -f $(@:%.o=%.Td) $(@:%.o=%.d)
 %/.sentinel:
 	@mkdir -p $* && touch $@
 
-include $(wildcard $(BUILD)/testRunner.d)
+include $(wildcard $(DRAGEN_OS_BUILD)/testRunner.d)
 
 # side effects:
 #  - builds 'libraries' variable required for linking programs, integration and system tests
@@ -68,7 +75,9 @@ programs_aux:=$(programs)
 include $(foreach program, $(programs), $(DRAGEN_OS_MAKE_DIR)/program.mk)
 
 # programs for system tests
+ifeq (1,${HAS_GTEST})
 include $(DRAGEN_OS_MAKE_DIR)/tests.mk
+endif
 
 include $(DRAGEN_OS_MAKE_DIR)/install.mk
 endif

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ Once you have bioconda installed, you should be able to install Dragmap with  `c
 
 Compilation was tested on CentOS 7
 
-* C++11 compatible compiler (e.g gcc-c++ >= 4.8.5-36.el7_6.2)
+* C++17 compatible compiler (e.g gcc-c++ >= 7.1)
 * GNU make >= 3.82
 * Boost library :  boost169-devel >= 1.69.0-1.el7
 * For unit tests : googletest (>= v1.6)

diff --git a/config.mk b/config.mk
@@ -27,8 +27,8 @@ endif
 #CC=$(GCC_BASE)/bin/gcc
 #CXX=$(GCC_BASE)/bin/g++
 
-CC=gcc
-CXX=g++
+CC?=gcc
+CXX?=g++
 
 ############################################################
 ##
@@ -84,7 +84,8 @@ endif # ifneq(,$(GTEST_ROOT))
 ##
 ############################################################
 
-SILENT?=$(if $(VERBOSE),,@)
+SILENT?=$(if $(VERBOSE),,@ $(ECHO) making $@; )
+SILENT_SE?=$(if $(VERBOSE),,@ $(ECHO) making $$@; )
 CAT?=cat
 ECHO?=echo
 EVAL?=eval
@@ -105,6 +106,7 @@ endif
 DRAGEN_THIRDPARTY?=$(DRAGEN_OS_ROOT_DIR)/thirdparty
 DRAGEN_SRC_DIR?=$(DRAGEN_OS_ROOT_DIR)/thirdparty/dragen/src
 DRAGEN_STUBS_DIR?=$(DRAGEN_OS_ROOT_DIR)/stubs/dragen/src
+BAMTOOLS_STUBS_DIR?=$(DRAGEN_OS_ROOT_DIR)/stubs/bamtools/bamtools-2.4.1
 SSW_SRC_DIR?=$(DRAGEN_OS_ROOT_DIR)/thirdparty/sswlib
 DRAGEN_OS_SRC_DIR?=$(DRAGEN_OS_ROOT_DIR)/src
 DRAGEN_OS_MAKE_DIR?=$(DRAGEN_OS_ROOT_DIR)/make
@@ -118,13 +120,13 @@ BUILD_TYPE=release
 endif
 # TODO: add support for differentiating by toolset
 DRAGEN_OS_BUILD_DIR?=$(DRAGEN_OS_BUILD_DIR_BASE)/$(BUILD_TYPE)
-BUILD:=$(DRAGEN_OS_BUILD_DIR)
+DRAGEN_OS_BUILD:=$(DRAGEN_OS_BUILD_DIR)
 
 ## List the libraries in the order where they should be statically linked
 DRAGEN_OS_LIBS := common options bam fastq sequences io reference map align workflow
 
 ## List the libraries from dragen source tree in the order where they should be statically linked
-DRAGEN_LIBS := common/hash_generation host/dragen_api/sampling common host/metrics
+DRAGEN_LIBS := common/hash_generation host/dragen_api/sampling common host/metrics host/infra/crypto
 
 ## List the libraries that pretend the dragen source tree libraries are being linked with rest of dragen source tree
 DRAGEN_STUB_LIBS := host/dragen_api host/metrics host/infra/linux
@@ -145,13 +147,18 @@ endif
 # version must be tagged in the git repo
 VERSION_STRING?=$(shell git describe --tags --always --abbrev=8 2> /dev/null || echo "UNKNOWN")
 
+CXXWARNINGS=-Werror -Wno-unused-variable -Wno-free-nonheap-object -Wno-parentheses
+CWARNINGS?=-Werror -Wno-unused-variable -Wno-unused-function -Wno-format-truncation
+CXXSTD?=-std=c++17
+
+
 CPPFLAGS?=-Wall -ggdb3
 #some dragen sources need this
 CPPFLAGS += -DLOCAL_BUILD
 CPPFLAGS += -D'DRAGEN_OS_VERSION="$(DRAGEN_OS_VERSION)"' 
 CPPFLAGS += -DVERSION_STRING="$(VERSION_STRING)"
-CXXFLAGS?=-std=c++11
-CFLAGS?=-std=c99 
+CXXFLAGS+=$(CXXWARNINGS) $(CXXSTD)
+CFLAGS+=$(CWARNINGS)
 LDFLAGS?=
 
 ifneq (,$(BOOST_INCLUDEDIR))
@@ -160,44 +167,57 @@ endif
 #CPPFLAGS += -I $(BAMTOOLS_INCLUDEDIR)
 CPPFLAGS += -I $(DRAGEN_THIRDPARTY)
 CPPFLAGS += -I $(DRAGEN_OS_SRC_DIR)/include
-CPPFLAGS += -I $(DRAGEN_SRC_DIR) -I $(DRAGEN_SRC_DIR)/common/public  -I $(DRAGEN_SRC_DIR)/host/metrics/public
+CPPFLAGS += -I $(DRAGEN_SRC_DIR) -I $(DRAGEN_SRC_DIR)/common/public -I $(DRAGEN_SRC_DIR)/host/dragen_api/sampling
+CPPFLAGS += -I $(DRAGEN_SRC_DIR)/host/infra/public -I $(DRAGEN_SRC_DIR)/host/metrics/public
 CPPFLAGS += -I $(SSW_SRC_DIR)
-CPPFLAGS += -I $(DRAGEN_STUBS_DIR)/host/dragen_api -I $(DRAGEN_STUBS_DIR)/host/dragen_api/dbam 
+CPPFLAGS += -I $(DRAGEN_STUBS_DIR)/host/dragen_api -I $(DRAGEN_STUBS_DIR)/host/dragen_api/dbam  
 CPPFLAGS += -I $(DRAGEN_STUBS_DIR)/host/infra/public -I $(DRAGEN_STUBS_DIR)/host/metrics/public
+CPPFLAGS += -I $(BAMTOOLS_STUBS_DIR)/include
 
 ifneq (,$(BOOST_LIBRARYDIR))
 LDFLAGS += -L $(BOOST_LIBRARYDIR)
 endif
 LDFLAGS += $(BOOST_LIBRARIES:%=-lboost_%)
 
+CPPFLAGS += -msse4.2 -mavx2 
 ifdef DEBUG
-CPPFLAGS += -O1 -ggdb3 -femit-class-debug-always -fno-omit-frame-pointer
+CPPFLAGS += -O0 -ggdb3 -femit-class-debug-always -fno-omit-frame-pointer
 ifeq ($(DEBUG),glibc)
 ifeq (,$(BOOST_LIBRARYDIR))
 $(error BOOST_LIBRARYDIR is not set. make sure that LD_LIBRARY_PATH and BOOST_LIBRARYDIR point to boost built with _GLIBCXX_DEBUG)
 endif #ifeq (,$(BOOST_LIBRARYDIR))
 CPPFLAGS += -D_GLIBCXX_DEBUG
 endif #ifeq ($(DEBUG),glibc)
-ifdef ASAN
-CPPFLAGS += -fsanitize=address
-ifeq ($(ASAN),all)
-CPPFLAGS += -fsanitize=leak -fsanitize=undefined # Not supported by g++ 4.8
-endif # ifeq ($(ASAN,all)
-endif # ASAN 
 #CPPFLAGS += -pg -fstack-usage -fprofile-arcs -ftest-coverage
 LDFLAGS += -lgcov -Wl,--exclude-libs=ALL
 else # non DEBUG
 #CPPFLAGS += -O3 -march=native # Not particularly great
 #CPPFLAGS += -O3 -march=skylake-avx512 # same as above
 
 # this seems to be fastest for fastq parsing. mainly because it manages to put proper PSUBB instruction for subtracing q0 from qscore chars
-CPPFLAGS += -Wfatal-errors -g -msse4.2 -O2 -ftree-vectorize -finline-functions -fpredictive-commoning -fgcse-after-reload -funswitch-loops -ftree-slp-vectorize -fvect-cost-model -fipa-cp-clone -ftree-phiprop
+CPPFLAGS += -g -O2 -ftree-vectorize -finline-functions -fpredictive-commoning -fgcse-after-reload -funswitch-loops -ftree-slp-vectorize -fvect-cost-model -fipa-cp-clone -ftree-phiprop
 
 # this seems slightly slower than above
 #CXXFLAGS += -g -mavx2 -O2 -ftree-vectorize -finline-functions -fpredictive-commoning -fgcse-after-reload -funswitch-loops -ftree-slp-vectorize -fvect-cost-model -fipa-cp-clone -ftree-phiprop
 endif # if DEBUG
 
-LDFLAGS+= -lz -lstdc++ -lrt -lgomp -lpthread
+ifdef ASAN
+CPPFLAGS += -fsanitize=address
+ifeq ($(ASAN),all)
+CPPFLAGS += -fsanitize=leak -fsanitize=undefined # Not supported by g++ 4.8
+endif # ifeq ($(ASAN,all)
+endif # ASAN 
+
+
+LDFLAGS+= -lz -lrt -lgomp -lpthread
+
+ifdef STATIC_LIBCPP
+LDFLAGS+= -static-libstdc++
+else
+LDFLAGS+= -lstdc++
+endif
+
+#LDFLAGS+= -lz -lstdc++ -lrt -lgomp -lpthread
 
 ifneq (,$(GTEST_INCLUDEDIR))
 GTEST_CPPFLAGS+= -I $(GTEST_INCLUDEDIR)
@@ -233,7 +253,7 @@ all_lib_sources := $(wildcard $(DRAGEN_OS_SRC_DIR)/lib/*/*.cpp)
 #all_lib_sources += $(wildcard $(DRAGEN_OS_SRC_DIR)/lib/*/*.c)
 found_lib_dirs := $(sort $(patsubst %/, %, $(dir $(all_lib_sources:$(DRAGEN_OS_SRC_DIR)/lib/%=%))))
 all_dragen_lib_sources += $(wildcard $(DRAGEN_SRC_DIR)/*/*/*.cpp) $(wildcard $(DRAGEN_SRC_DIR)/*/*/*/*.cpp)
-all_dragen_lib_sources += $(wildcard $(DRAGEN_SRC_DIR)/*/*/*.c)
+all_dragen_lib_sources += $(wildcard $(DRAGEN_SRC_DIR)/*/*/*.c) $(wildcard $(DRAGEN_SRC_DIR)/*/*/*/*.c)
 found_dragen_lib_dirs := $(sort $(patsubst %/, %, $(dir $(all_dragen_lib_sources:$(DRAGEN_SRC_DIR)/%=%))))
 ifneq ($(sort $(DRAGEN_OS_LIBS) $(DRAGEN_LIBS)),$(sort $(found_lib_dirs) $(found_dragen_lib_dirs)))
 $(error found libraries: $(sort $(found_dragen_lib_dirs) $(found_lib_dirs)): expected libraries: $(sort $(DRAGEN_OS_LIBS) $(DRAGEN_LIBS)): verify that the DRAGEN_OS_LIBS and DRAGEN_LIBS variables in config.mk lists the correct libraries)

diff --git a/make/compare.mk b/make/compare.mk
diff --git a/make/dragen_lib.mk b/make/dragen_lib.mk
@@ -14,8 +14,8 @@ endif
 
 lib_sources := $(wildcard $(DRAGEN_SRC_DIR)/$(lib_dir)/*.cpp)
 lib_c_sources := $(wildcard $(DRAGEN_SRC_DIR)/$(lib_dir)/*.c)
-lib_objects := $(lib_sources:$(DRAGEN_SRC_DIR)/$(lib_dir)/%.cpp=$(BUILD)/drgn_$(lib_dir)/%.o)
-lib_objects += $(lib_c_sources:$(DRAGEN_SRC_DIR)/$(lib_dir)/%.c=$(BUILD)/drgn_$(lib_dir)/%.o)
+lib_objects := $(lib_sources:$(DRAGEN_SRC_DIR)/$(lib_dir)/%.cpp=$(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/%.o)
+lib_objects += $(lib_c_sources:$(DRAGEN_SRC_DIR)/$(lib_dir)/%.c=$(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/%.o)
 
 include $(wildcard $(lib_objects:%.o=%.d))
 
@@ -24,28 +24,22 @@ include $(wildcard $(lib_objects:%.o=%.d))
 #
 #
 ###
-$(BUILD)/drgn_$(lib_dir).a: lib_objects:=$(lib_objects)
-$(BUILD)/drgn_$(lib_dir).a: $(lib_objects)
-	$(AR) crfs $@ $(lib_objects)
-
-#$(BUILD)/$(lib_dir)/%.o: $(DRAGEN_OS_SRC_DIR)/lib/$(lib_dir)/%.cpp $(BUILD)/$(lib_dir)/%.d $(BUILD)/$(lib_dir)/.sentinel
-#	$(CXX) $(DEPFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<
-#	$(POSTCOMPILE)
+$(DRAGEN_OS_BUILD)/drgn_$(lib_dir).a: lib_objects:=$(lib_objects)
+$(DRAGEN_OS_BUILD)/drgn_$(lib_dir).a: $(lib_objects)
+	$(SILENT) $(AR) crfs $@ $(lib_objects)
 
 # Note: the dependency on $(libraries) is to force the order of compilation to be the same as the order of declaration of the libraries
-$(BUILD)/drgn_$(lib_dir)/%.o: lib_dir:=$(lib_dir)
-$(BUILD)/drgn_$(lib_dir)/%.o: $(DRAGEN_SRC_DIR)/$(lib_dir)/%.cpp $(BUILD)/drgn_$(lib_dir)/%.d $(BUILD)/drgn_$(lib_dir)/.sentinel $(libraries)
-	$(CXX) $(DEPFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DRAGEN_OS_FLAGS) -c -o $@ $<
-	$(POSTCOMPILE)
+$(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/%.o: lib_dir:=$(lib_dir)
+$(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/%.o: $(DRAGEN_SRC_DIR)/$(lib_dir)/%.cpp $(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/%.d $(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/.sentinel
+	$(SILENT) $(CXX) $(DEPFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DRAGEN_OS_FLAGS) -c -o $@ $< && $(POSTCOMPILE)
 
-$(BUILD)/drgn_$(lib_dir)/%.o: $(DRAGEN_SRC_DIR)/$(lib_dir)/%.c $(BUILD)/drgn_$(lib_dir)/%.d $(BUILD)/drgn_$(lib_dir)/.sentinel $(libraries)
-	$(CC) $(DEPFLAGS) $(CPPFLAGS) $(CFLAGS) $(DRAGEN_OS_FLAGS) -c -o $@ $<
-	$(POSTCOMPILE)
+$(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/%.o: $(DRAGEN_SRC_DIR)/$(lib_dir)/%.c $(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/%.d $(DRAGEN_OS_BUILD)/drgn_$(lib_dir)/.sentinel
+	$(SILENT) $(CC) $(DEPFLAGS) $(CPPFLAGS) $(CFLAGS) $(DRAGEN_OS_FLAGS) -c -o $@ $< && $(POSTCOMPILE)
 
-#$(BUILD)/$(lib_dir)/%.d: ;
+#$(DRAGEN_OS_BUILD)/$(lib_dir)/%.d: ;
 
 
 ###
 # must be built in reverse order for linking
 ###
-libraries := $(BUILD)/drgn_$(lib_dir).a $(libraries)
+libraries := $(DRAGEN_OS_BUILD)/drgn_$(lib_dir).a $(libraries)
diff --git a/make/dragen_stub_lib.mk b/make/dragen_stub_lib.mk
@@ -12,8 +12,8 @@ endif
 
 lib_sources := $(wildcard $(DRAGEN_STUBS_DIR)/$(lib_dir)/*.cpp)
 lib_c_sources := $(wildcard $(DRAGEN_STUBS_DIR)/$(lib_dir)/*.c)
-lib_objects := $(lib_sources:$(DRAGEN_STUBS_DIR)/$(lib_dir)/%.cpp=$(BUILD)/stub_$(lib_dir)/%.o)
-lib_objects += $(lib_c_sources:$(DRAGEN_STUBS_DIR)/$(lib_dir)/%.c=$(BUILD)/stub_$(lib_dir)/%.o)
+lib_objects := $(lib_sources:$(DRAGEN_STUBS_DIR)/$(lib_dir)/%.cpp=$(DRAGEN_OS_BUILD)/stub_$(lib_dir)/%.o)
+lib_objects += $(lib_c_sources:$(DRAGEN_STUBS_DIR)/$(lib_dir)/%.c=$(DRAGEN_OS_BUILD)/stub_$(lib_dir)/%.o)
 
 include $(wildcard $(lib_objects:%.o=%.d))
 
@@ -22,28 +22,26 @@ include $(wildcard $(lib_objects:%.o=%.d))
 #
 #
 ###
-$(BUILD)/stub_$(lib_dir).a: lib_objects:=$(lib_objects)
-$(BUILD)/stub_$(lib_dir).a: $(lib_objects)
-	$(AR) crfs $@ $(lib_objects)
+$(DRAGEN_OS_BUILD)/stub_$(lib_dir).a: lib_objects:=$(lib_objects)
+$(DRAGEN_OS_BUILD)/stub_$(lib_dir).a: $(lib_objects)
+	$(SILENT) $(AR) crfs $@ $(lib_objects)
 
-#$(BUILD)/$(lib_dir)/%.o: $(DRAGEN_OS_SRC_DIR)/lib/$(lib_dir)/%.cpp $(BUILD)/$(lib_dir)/%.d $(BUILD)/$(lib_dir)/.sentinel
+#$(DRAGEN_OS_BUILD)/$(lib_dir)/%.o: $(DRAGEN_OS_SRC_DIR)/lib/$(lib_dir)/%.cpp $(DRAGEN_OS_BUILD)/$(lib_dir)/%.d $(DRAGEN_OS_BUILD)/$(lib_dir)/.sentinel
 #	$(CXX) $(DEPFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<
 #	$(POSTCOMPILE)
 
 # Note: the dependency on $(libraries) is to force the order of compilation to be the same as the order of declaration of the libraries
-$(BUILD)/stub_$(lib_dir)/%.o: lib_dir:=$(lib_dir)
-$(BUILD)/stub_$(lib_dir)/%.o: $(DRAGEN_STUBS_DIR)/$(lib_dir)/%.cpp $(BUILD)/stub_$(lib_dir)/%.d $(BUILD)/stub_$(lib_dir)/.sentinel $(libraries)
-	$(CXX) $(DEPFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<
-	$(POSTCOMPILE)
+$(DRAGEN_OS_BUILD)/stub_$(lib_dir)/%.o: lib_dir:=$(lib_dir)
+$(DRAGEN_OS_BUILD)/stub_$(lib_dir)/%.o: $(DRAGEN_STUBS_DIR)/$(lib_dir)/%.cpp $(DRAGEN_OS_BUILD)/stub_$(lib_dir)/%.d $(DRAGEN_OS_BUILD)/stub_$(lib_dir)/.sentinel
+	$(SILENT) $(CXX) $(DEPFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $< && $(POSTCOMPILE)
 
-$(BUILD)/stub_$(lib_dir)/%.o: $(DRAGEN_STUBS_DIR)/stub_$(lib_dir)/%.c $(BUILD)/$(lib_dir)/%.d $(BUILD)/stub_$(lib_dir)/.sentinel $(libraries)
-	$(CC) $(DEPFLAGS) $(CPPFLAGS) $(CFLAGS) -c -o $@ $<
-	$(POSTCOMPILE)
+$(DRAGEN_OS_BUILD)/stub_$(lib_dir)/%.o: $(DRAGEN_STUBS_DIR)/stub_$(lib_dir)/%.c $(DRAGEN_OS_BUILD)/$(lib_dir)/%.d $(DRAGEN_OS_BUILD)/stub_$(lib_dir)/.sentinel
+	$(SILENT) $(CC) $(DEPFLAGS) $(CPPFLAGS) $(CFLAGS) -c -o $@ $< && $(POSTCOMPILE)
 
-#$(BUILD)/$(lib_dir)/%.d: ;
+#$(DRAGEN_OS_BUILD)/$(lib_dir)/%.d: ;
 
 
 ###
 # must be built in reverse order for linking
 ###
-libraries := $(BUILD)/stub_$(lib_dir).a $(libraries)
+libraries := $(DRAGEN_OS_BUILD)/stub_$(lib_dir).a $(libraries)
diff --git a/make/install.mk b/make/install.mk
@@ -4,6 +4,6 @@ bindir?=/bin
 
 install: $(programs:%=install_%)
 
-install_%: $(BUILD)/%
+install_%: $(DRAGEN_OS_BUILD)/%
 	$(INSTALL) $<  $(DESTDIR)$(bindir)/$*