FMAlign2/Makefile at master · pinglu-zhang/FMAlign2 · GitHub

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
# compilers
CXX     = g++
CC      = gcc

# toggle: 1 = static (default), 0 = dynamic
STATIC_LINK ?= 1

# detect OS
UNAME_S := $(shell uname -s)

# flags (compile)
CXXFLAGS = -Wall -std=c++17 -Iinclude
CFLAGS   = -Iinclude

# flags (link)
LDFLAGS  =
LDLIBS   =

SRCS = main.cpp \
       src/utils.cpp \
       src/mem_finder.cpp \
       src/sequence_split_align.cpp \
       src/ssw.cpp \
       src/ssw_cpp.cpp

# non-Windows extra sources
ifeq ($(OS),Windows_NT)
    # OpenMP（按需）
    CXXFLAGS += -fopenmp
else
    SRCS += src/thread_pool.cpp src/thread_condition.cpp
    # POSIX 线程
    CXXFLAGS += -pthread
    # Linux 专用 rt（macOS 没有）
    ifeq ($(UNAME_S),Linux)
        LDLIBS += -lrt
    endif
endif

# link mode: default static (Linux)
ifeq ($(STATIC_LINK),1)
  ifeq ($(UNAME_S),Linux)
    # 静态链接（需要对应的静态库已安装）
    LDFLAGS += -static -static-libstdc++ -static-libgcc
    # pthread 静态：确保完整吸入
    LDLIBS  += -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
  else
    $(warning Static linking is not supported on $(UNAME_S); falling back to dynamic)
    LDFLAGS += -pthread
  endif
else
  # 动态链接
  LDFLAGS += -pthread
endif

# C sources
CSRCS = src/gsacak.c

OBJS  = $(SRCS:.cpp=.o) $(CSRCS:.c=.o)

# debug / release
ifdef DEBUG
    CXXFLAGS += -O0 -g -DDEBUG
    CFLAGS   += -O0 -g
else
    CXXFLAGS += -O3
    CFLAGS   += -O3
endif

# 64-bit macro
ifdef M64
    CXXFLAGS += -DM64
    CFLAGS   += -DM64
endif

# default target
all: fmalign2

# final target
fmalign2: $(OBJS)
	$(CXX) $(LDFLAGS) $(OBJS) $(LDLIBS) -o $@

# generic rules
%.o: %.cpp
	$(CXX) $(CXXFLAGS) -c $< -o $@

%.o: %.c
	$(CC) $(CFLAGS) -c $< -o $@

# ---------- install/uninstall ----------
PREFIX  ?= /usr/local
BINDIR  ?= $(PREFIX)/bin
INSTALL ?= install

.PHONY: install uninstall

install: fmalign2
	$(INSTALL) -d "$(DESTDIR)$(BINDIR)"
	$(INSTALL) -m 0755 fmalign2 "$(DESTDIR)$(BINDIR)/fmalign2"

uninstall:
	rm -f "$(DESTDIR)$(BINDIR)/fmalign2"

# ---------- clean ----------
.PHONY: clean
clean:
ifeq ($(OS),Windows_NT)
	- del /f $(subst /,\\,$(OBJS)) 2> NUL
	- del /f fmalign2.exe 2> NUL
else
	rm -f $(OBJS) fmalign2
endif