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#
# Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
#
# This file is part of HISAT 2.
#
# HISAT 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# HISAT 2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
#
JAVA_HOME := $(JAVA_HOME)
HISAT2_DIR = ../..
CC = gcc
MACOS = 0
ifneq (,$(findstring Darwin,$(shell uname)))
MACOS = 1
endif
INCLUDES = -I $(JAVA_HOME)/include
INCLUDES += -I $(JAVA_HOME)/include/linux
TARGET_LIB = libht2jni.so
SHARED_FLAG = -shared
ifeq (1,$(MACOS))
INCLUDES += -I $(JAVA_HOME)/include/darwin
TARGET_LIB = libht2jni.jnilib
SHARED_FLAG = -dynamiclib
endif
INCLUDES += -I $(HISAT2_DIR)/hisat2lib
CFLAGS = -fPIC $(INCLUDES)
#CFLAGS += -DDEBUG
SRCS = ht2module.c
OBJS = $(SRCS:.c=.o)
all: lib
lib: $(TARGET_LIB)
$(TARGET_LIB): HT2Module.h $(OBJS)
$(CC) $(SHARED_FLAG) -o $@ $(OBJS) $(HISAT2_DIR)/libhisat2lib.a -lstdc++
HT2Module.h HT2Module.class: HT2Module.java
javac -h . HT2Module.java
example: HT2ModuleExample.class
HT2ModuleExample.class: HT2ModuleExample.java
javac HT2ModuleExample.java
clean:
rm -f *.class HT2Module.h HT2Module_HT2Position.h *.so *.o $(TARGET_LIB)
test: all example
java -Djava.library.path=. HT2ModuleExample
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