1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
|
#-- for now these MUST point to the included "samtools-0.x.x" and "gclib" sub-directories
GDIR := ./gclib
#--
INCDIRS := -I. -I${GDIR} -I/usr/include/samtools -I/usr/include/htslib
CXX := $(if $(CXX),$(CXX),g++)
BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
-D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti
#for gcc 8+ add: -Wno-class-memaccess
GCCVER5 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 5)
ifeq "$(GCCVER5)" "1"
BASEFLAGS += -Wno-implicit-fallthrough
endif
GCCVER8 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 8)
ifeq "$(GCCVER8)" "1"
BASEFLAGS += -Wno-class-memaccess
endif
LINKER := $(if $(LINKER),$(LINKER),g++)
LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
LIBS := -lhts -lbam -lz
ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
NOTHREADS=1
endif
#detect MinGW (Windows environment)
ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine)))
WINDOWS=1
endif
# Misc. system commands
ifdef WINDOWS
RM = del /Q
else
RM = rm -f
endif
# File endings
ifdef WINDOWS
EXE = .exe
else
EXE =
endif
# Non-windows systems need pthread
ifndef WINDOWS
ifndef NOTHREADS
LIBS := -pthread ${LIBS}
BASEFLAGS += -pthread
endif
endif
ifdef NOTHREADS
BASEFLAGS += -DNOTHREADS
endif
DMACH := $(shell ${CXX} -dumpmachine)
ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
# -- release build
RELEASE_BUILD=1
CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O3)
CXXFLAGS += -DNDEBUG $(BASEFLAGS)
else
ifneq (,$(filter %memcheck %memdebug %tsan %tcheck %thrcheck, $(MAKECMDGOALS)))
#use sanitizer in gcc 4.9+
GCCVER49 := $(shell expr `${CXX} -dumpversion | cut -f1,2 -d.` \>= 4.9)
ifeq "$(GCCVER49)" "0"
$(error gcc version 4.9 or greater is required for this build target)
endif
CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
SANLIBS :=
ifneq (,$(filter %tsan %tcheck %thrcheck, $(MAKECMDGOALS)))
# thread sanitizer only (incompatible with address sanitizer)
CXXFLAGS += -fno-omit-frame-pointer -fsanitize=thread -fsanitize=undefined $(BASEFLAGS)
SANLIBS := -ltsan
else
# address sanitizer
CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address $(BASEFLAGS)
SANLIBS := -lasan
endif
ifeq "$(GCCVER5)" "1"
CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr
CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
#CXXFLAGS += -fcheck-pointer-bounds -mmpx
endif
CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
LIBS := ${SANLIBS} -lubsan -ldl ${LIBS}
else
#just plain debug build
DEBUG_BUILD=1
CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-g -O0)
#CXXFLAGS := $(if $(CXXFLAGS),$(CXXFLAGS),-ggdb -g3 -O0 -fvar-tracking-assignments -fno-omit-frame-pointer)
ifneq (, $(findstring darwin, $(DMACH)))
CXXFLAGS += -gdwarf-3
endif
CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
endif
endif
ifdef RELEASE_BUILD
ifneq (,$(findstring static, $(MAKECMDGOALS)))
STATIC_CLIB=1
endif
endif
ifdef STATIC_CLIB
LDFLAGS += -static-libgcc -static-libstdc++
endif
ifdef DEBUG_BUILD
#$(warning Building DEBUG version of stringtie.. )
DBG_WARN=@echo
DBG_WARN+='WARNING: built DEBUG version [much slower], use "make clean release" for a faster, optimized version of the program.'
endif
OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \
${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFastaIndex.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o
ifneq (,$(filter %memtrace %memusage %memuse, $(MAKECMDGOALS)))
CXXFLAGS += -DGMEMTRACE
OBJS += ${GDIR}/proc_mem.o
endif
ifndef NOTHREADS
OBJS += ${GDIR}/GThreads.o
endif
%.o : %.cpp
${CXX} ${CXXFLAGS} -c $< -o $@
OBJS += rlink.o tablemaker.o tmerge.o
all release static debug: stringtie${EXE}
memcheck memdebug tsan tcheck thrcheck: stringtie${EXE}
memuse memusage memtrace: stringtie${EXE}
nothreads: stringtie${EXE}
${GDIR}/GBam.o : $(GDIR)/GBam.h
stringtie.o : $(GDIR)/GBitVec.h $(GDIR)/GHash.hh $(GDIR)/GBam.h
rlink.o : rlink.h tablemaker.h $(GDIR)/GBam.h $(GDIR)/GBitVec.h
tmerge.o : rlink.h tmerge.h
tablemaker.o : tablemaker.h rlink.h
stringtie: $(OBJS) stringtie.o
${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
@echo
${DBG_WARN}
test demo tests: stringtie${EXE}
@./run_tests.sh
.PHONY : clean cleanall cleanAll allclean
# target for removing all object files
# echo $(PATH)
clean:
${RM} stringtie${EXE} stringtie.o* $(OBJS)
${RM} core.*
allclean cleanAll cleanall:
${RM} stringtie${EXE} stringtie.o* $(OBJS)
${RM} core.*
|
