591 lines
16 KiB
Makefile
591 lines
16 KiB
Makefile
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#
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# Copyright 2015, Daehwan Kim <infphilo@gmail.com>
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#
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# This file is part of HISAT2.
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#
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# HISAT 2 is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# HISAT 2 is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with HISAT. If not, see <http://www.gnu.org/licenses/>.
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#
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#
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# Makefile for hisat2-align, hisat2-build, hisat2-inspect
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#
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INC =
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GCC_PREFIX = $(shell dirname `which gcc`)
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GCC_SUFFIX =
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CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
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CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
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CXX = $(CPP)
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HEADERS = $(wildcard *.h)
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BOWTIE_MM = 1
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BOWTIE_SHARED_MEM = 0
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# Detect Cygwin or MinGW
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WINDOWS = 0
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CYGWIN = 0
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MINGW = 0
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ifneq (,$(findstring CYGWIN,$(shell uname)))
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WINDOWS = 1
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CYGWIN = 1
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# POSIX memory-mapped files not currently supported on Windows
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BOWTIE_MM = 0
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BOWTIE_SHARED_MEM = 0
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else
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ifneq (,$(findstring MINGW,$(shell uname)))
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WINDOWS = 1
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MINGW = 1
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# POSIX memory-mapped files not currently supported on Windows
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BOWTIE_MM = 0
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BOWTIE_SHARED_MEM = 0
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endif
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endif
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MACOS = 0
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ifneq (,$(findstring Darwin,$(shell uname)))
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MACOS = 1
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endif
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EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11
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INC += -I. -I third_party
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MM_DEF =
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ifeq (1,$(BOWTIE_MM))
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MM_DEF = -DBOWTIE_MM
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endif
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SHMEM_DEF =
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ifeq (1,$(BOWTIE_SHARED_MEM))
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SHMEM_DEF = -DBOWTIE_SHARED_MEM
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endif
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PTHREAD_PKG =
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PTHREAD_LIB =
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ifeq (1,$(MINGW))
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PTHREAD_LIB =
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else
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PTHREAD_LIB = -lpthread
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endif
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SEARCH_LIBS =
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BUILD_LIBS =
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INSPECT_LIBS =
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ifeq (1,$(MINGW))
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BUILD_LIBS =
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INSPECT_LIBS =
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endif
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USE_SRA = 0
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SRA_DEF =
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SRA_LIB =
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SERACH_INC =
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ifeq (1,$(USE_SRA))
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SRA_DEF = -DUSE_SRA
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SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl
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SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include
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SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
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endif
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LIBS = $(PTHREAD_LIB)
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HT2LIB_DIR = hisat2lib
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HT2LIB_CPPS = $(HT2LIB_DIR)/ht2_init.cpp \
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$(HT2LIB_DIR)/ht2_repeat.cpp \
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$(HT2LIB_DIR)/ht2_index.cpp
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SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
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edit.cpp gfm.cpp \
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reference.cpp ds.cpp multikey_qsort.cpp limit.cpp \
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random_source.cpp tinythread.cpp utility_3n.cpp
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SEARCH_CPPS = qual.cpp pat.cpp \
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read_qseq.cpp aligner_seed_policy.cpp \
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aligner_seed.cpp \
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aligner_seed2.cpp \
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aligner_sw.cpp \
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aligner_sw_driver.cpp aligner_cache.cpp \
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aligner_result.cpp ref_coord.cpp mask.cpp \
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pe.cpp aln_sink.cpp dp_framer.cpp \
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scoring.cpp presets.cpp unique.cpp \
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simple_func.cpp \
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random_util.cpp \
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aligner_bt.cpp sse_util.cpp \
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aligner_swsse.cpp outq.cpp \
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aligner_swsse_loc_i16.cpp \
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aligner_swsse_ee_i16.cpp \
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aligner_swsse_loc_u8.cpp \
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aligner_swsse_ee_u8.cpp \
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aligner_driver.cpp \
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splice_site.cpp \
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alignment_3n.cpp \
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position_3n.cpp \
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$(HT2LIB_CPPS)
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BUILD_CPPS = diff_sample.cpp
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REPEAT_CPPS = \
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mask.cpp \
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qual.cpp \
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aligner_bt.cpp \
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scoring.cpp \
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simple_func.cpp \
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dp_framer.cpp \
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aligner_result.cpp \
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aligner_sw_driver.cpp \
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aligner_sw.cpp \
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aligner_swsse_ee_i16.cpp \
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aligner_swsse_ee_u8.cpp \
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aligner_swsse_loc_i16.cpp \
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aligner_swsse_loc_u8.cpp \
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aligner_swsse.cpp \
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bit_packed_array.cpp \
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repeat_builder.cpp
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THREE_N_HEADERS = \
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position_3n_table.h \
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alignment_3n_table.h \
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utility_3n_table.h
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HISAT2_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp
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HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp
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HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS) hisat2_repeat_main.cpp
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SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
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VERSION := $(shell cat HISAT2_VERSION)
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# Convert BITS=?? to a -m flag
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BITS=32
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ifeq (x86_64,$(shell uname -m))
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BITS=64
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endif
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# msys will always be 32 bit so look at the cpu arch instead.
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ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
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ifeq (1,$(MINGW))
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BITS=64
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endif
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endif
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BITS_FLAG =
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ifeq (32,$(BITS))
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BITS_FLAG = -m32
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endif
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ifeq (64,$(BITS))
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BITS_FLAG = -m64
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endif
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SSE_FLAG=-msse2
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DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
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DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
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RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
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RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
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NOASSERT_FLAGS = -DNDEBUG
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FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
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HT2LIB_FLAGS = -DHISAT2_BUILD_LIB
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ifeq (1,$(USE_SRA))
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ifeq (1, $(MACOS))
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SRA_LIB += -stdlib=libc++
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DEBUG_FLAGS += -mmacosx-version-min=10.10
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RELEASE_FLAGS += -mmacosx-version-min=10.10
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endif
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endif
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HISAT2_BIN_LIST = hisat2-build-s \
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hisat2-build-l \
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hisat2-align-s \
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hisat2-align-l \
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hisat2-inspect-s \
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hisat2-inspect-l \
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hisat2-repeat \
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hisat-3n-table
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HISAT2_BIN_LIST_AUX = hisat2-build-s-debug \
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hisat2-build-l-debug \
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hisat2-align-s-debug \
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hisat2-align-l-debug \
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hisat2-inspect-s-debug \
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hisat2-inspect-l-debug \
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hisat2-repeat-debug
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HT2LIB_SRCS = $(SHARED_CPPS) \
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$(HT2LIB_CPPS)
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HT2LIB_OBJS = $(HT2LIB_SRCS:.cpp=.o)
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HT2LIB_DEBUG_OBJS = $(addprefix .ht2lib-obj-debug/,$(HT2LIB_OBJS))
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HT2LIB_RELEASE_OBJS = $(addprefix .ht2lib-obj-release/,$(HT2LIB_OBJS))
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HT2LIB_SHARED_DEBUG_OBJS = $(addprefix .ht2lib-obj-debug-shared/,$(HT2LIB_OBJS))
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HT2LIB_SHARED_RELEASE_OBJS = $(addprefix .ht2lib-obj-release-shared/,$(HT2LIB_OBJS))
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HT2LIB_PKG_SRC = \
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$(HT2LIB_DIR)/ht2_init.cpp \
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$(HT2LIB_DIR)/ht2_repeat.cpp \
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$(HT2LIB_DIR)/ht2_index.cpp \
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$(HT2LIB_DIR)/ht2.h \
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$(HT2LIB_DIR)/ht2_handle.h \
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$(HT2LIB_DIR)/java_jni/Makefile \
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$(HT2LIB_DIR)/java_jni/ht2module.c \
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$(HT2LIB_DIR)/java_jni/HT2Module.java \
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$(HT2LIB_DIR)/java_jni/HT2ModuleExample.java \
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$(HT2LIB_DIR)/pymodule/Makefile \
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$(HT2LIB_DIR)/pymodule/ht2module.c \
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$(HT2LIB_DIR)/pymodule/setup.py \
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$(HT2LIB_DIR)/pymodule/ht2example.py
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GENERAL_LIST = $(wildcard scripts/*.sh) \
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$(wildcard scripts/*.pl) \
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$(wildcard *.py) \
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$(wildcard example/index/*.ht2) \
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$(wildcard example/reads/*.fa) \
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example/reference/22_20-21M.fa \
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example/reference/22_20-21M.snp \
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$(PTHREAD_PKG) \
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hisat2 \
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hisat2-build \
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hisat2-inspect \
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AUTHORS \
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LICENSE \
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NEWS \
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MANUAL \
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MANUAL.markdown \
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TUTORIAL \
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HISAT2_VERSION
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ifeq (1,$(WINDOWS))
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HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat
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endif
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# This is helpful on Windows under MinGW/MSYS, where Make might go for
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# the Windows FIND tool instead.
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FIND=$(shell which find)
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SRC_PKG_LIST = $(wildcard *.h) \
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$(wildcard *.hh) \
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$(wildcard *.c) \
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$(wildcard *.cpp) \
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$(HT2LIB_PKG_SRC) \
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Makefile \
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CMakeLists.txt \
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$(GENERAL_LIST)
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BIN_PKG_LIST = $(GENERAL_LIST)
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.PHONY: all allall both both-debug
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all: $(HISAT2_BIN_LIST)
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allall: $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)
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both: hisat2-align-s hisat2-align-l hisat2-build-s hisat2-build-l
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both-debug: hisat2-align-s-debug hisat2-align-l-debug hisat2-build-s-debug hisat2-build-l-debug
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repeat: hisat2-repeat
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repeat-debug: hisat2-repeat-debug
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DEFS :=-fno-strict-aliasing \
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-DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" \
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-DBUILD_HOST="\"`hostname`\"" \
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-DBUILD_TIME="\"`date`\"" \
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-DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
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$(FILE_FLAGS) \
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$(PREF_DEF) \
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$(MM_DEF) \
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$(SHMEM_DEF)
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#
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# hisat-bp targets
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#
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hisat-bp-bin: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
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$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
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$(LIBS) $(SEARCH_LIBS)
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hisat-bp-bin-debug: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
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$(CXX) $(DEBUG_FLAGS) \
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$(DEBUG_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 -Wall \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
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$(LIBS) $(SEARCH_LIBS)
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#
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# hisat2-repeat targets
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#
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hisat2-repeat: hisat2_repeat.cpp $(REPEAT_CPPS) $(SHARED_CPPS) $(HEADERS)
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$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_REPEAT_CPPS_MAIN) \
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$(LIBS) $(BUILD_LIBS)
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hisat2-repeat-debug: hisat2_repeat.cpp $(REPEAT_CPPS) $(SHARED_CPPS) $(HEADERS)
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$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
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$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
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$(INC) \
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-o $@ $< \
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$(SHARED_CPPS) $(HISAT2_REPEAT_CPPS_MAIN) \
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$(LIBS) $(BUILD_LIBS)
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|
||
|
|
|
||
|
|
#
|
||
|
|
# hisat2-build targets
|
||
|
|
#
|
||
|
|
|
||
|
|
hisat2-build-s: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
|
||
|
|
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall -DMASSIVE_DATA_RLCSA \
|
||
|
|
$(INC) \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
|
||
|
|
$(LIBS) $(BUILD_LIBS)
|
||
|
|
|
||
|
|
hisat2-build-l: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
|
||
|
|
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
|
||
|
|
$(INC) \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
|
||
|
|
$(LIBS) $(BUILD_LIBS)
|
||
|
|
|
||
|
|
hisat2-build-s-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
|
||
|
|
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) -DBOWTIE2 -Wall -DMASSIVE_DATA_RLCSA \
|
||
|
|
$(INC) \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
|
||
|
|
$(LIBS) $(BUILD_LIBS)
|
||
|
|
|
||
|
|
hisat2-build-l-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
|
||
|
|
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
|
||
|
|
$(INC) \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
|
||
|
|
$(LIBS) $(BUILD_LIBS)
|
||
|
|
|
||
|
|
#
|
||
|
|
# hisat2 targets
|
||
|
|
#
|
||
|
|
|
||
|
|
hisat2-align-s: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
|
||
|
|
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) $(SRA_DEF) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
|
||
|
|
$(INC) $(SEARCH_INC) \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
|
||
|
|
$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
|
||
|
|
|
||
|
|
hisat2-align-l: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
|
||
|
|
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
|
||
|
|
$(INC) $(SEARCH_INC) \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
|
||
|
|
$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
|
||
|
|
|
||
|
|
hisat2-align-s-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
|
||
|
|
$(CXX) $(DEBUG_FLAGS) \
|
||
|
|
$(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) $(SRA_DEF) -DBOWTIE2 -Wall \
|
||
|
|
$(INC) $(SEARCH_INC) \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
|
||
|
|
$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
|
||
|
|
|
||
|
|
hisat2-align-l-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
|
||
|
|
$(CXX) $(DEBUG_FLAGS) \
|
||
|
|
$(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
|
||
|
|
$(INC) $(SEARCH_INC) \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
|
||
|
|
$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
|
||
|
|
|
||
|
|
#
|
||
|
|
# hisat2-inspect targets
|
||
|
|
#
|
||
|
|
|
||
|
|
hisat2-inspect-s: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
|
||
|
|
$(CXX) $(RELEASE_FLAGS) \
|
||
|
|
$(RELEASE_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \
|
||
|
|
$(INC) -I . \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) \
|
||
|
|
$(LIBS) $(INSPECT_LIBS)
|
||
|
|
|
||
|
|
hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
|
||
|
|
$(CXX) $(RELEASE_FLAGS) \
|
||
|
|
$(RELEASE_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \
|
||
|
|
$(INC) -I . \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) \
|
||
|
|
$(LIBS) $(INSPECT_LIBS)
|
||
|
|
|
||
|
|
hisat2-inspect-s-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
|
||
|
|
$(CXX) $(DEBUG_FLAGS) \
|
||
|
|
$(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \
|
||
|
|
$(INC) -I . \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) \
|
||
|
|
$(LIBS) $(INSPECT_LIBS)
|
||
|
|
|
||
|
|
hisat2-inspect-l-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
|
||
|
|
$(CXX) $(DEBUG_FLAGS) \
|
||
|
|
$(DEBUG_DEFS) $(EXTRA_FLAGS) \
|
||
|
|
$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \
|
||
|
|
$(INC) -I . \
|
||
|
|
-o $@ $< \
|
||
|
|
$(SHARED_CPPS) \
|
||
|
|
$(LIBS) $(INSPECT_LIBS)
|
||
|
|
|
||
|
|
#
|
||
|
|
# hisat-3n-table targets
|
||
|
|
#
|
||
|
|
|
||
|
|
hisat-3n-table: hisat_3n_table.cpp $(THREE_N_HEADERS)
|
||
|
|
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) $(NOASSERT_FLAGS) $(DEFS) -pthread -o $@ $<
|
||
|
|
|
||
|
|
#
|
||
|
|
# HT2LIB targets
|
||
|
|
#
|
||
|
|
|
||
|
|
ht2lib: libhisat2lib-debug.a libhisat2lib.a libhisat2lib-debug.so libhisat2lib.so
|
||
|
|
|
||
|
|
libhisat2lib-debug.a: $(HT2LIB_DEBUG_OBJS)
|
||
|
|
ar rc $@ $(HT2LIB_DEBUG_OBJS)
|
||
|
|
|
||
|
|
libhisat2lib.a: $(HT2LIB_RELEASE_OBJS)
|
||
|
|
ar rc $@ $(HT2LIB_RELEASE_OBJS)
|
||
|
|
|
||
|
|
libhisat2lib-debug.so: $(HT2LIB_SHARED_DEBUG_OBJS)
|
||
|
|
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) $(DEFS) $(SRA_DEF) -DBOWTIE2 -Wall $(INC) $(SEARCH_INC) \
|
||
|
|
-shared -o $@ $(HT2LIB_SHARED_DEBUG_OBJS) $(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
|
||
|
|
|
||
|
|
libhisat2lib.so: $(HT2LIB_SHARED_RELEASE_OBJS)
|
||
|
|
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) $(DEFS) $(SRA_DEF) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall $(INC) $(SEARCH_INC)\
|
||
|
|
-shared -o $@ $(HT2LIB_SHARED_RELEASE_OBJS) $(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
|
||
|
|
|
||
|
|
.ht2lib-obj-debug/%.o: %.cpp
|
||
|
|
@mkdir -p $(dir $@)/$(dir $<)
|
||
|
|
$(CXX) -fPIC $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) $(DEFS) $(SRA_DEF) $(HT2LIB_FLAGS) -DBOWTIE2 -Wall $(INC) $(SEARCH_INC) \
|
||
|
|
-c -o $@ $<
|
||
|
|
|
||
|
|
.ht2lib-obj-release/%.o: %.cpp
|
||
|
|
@mkdir -p $(dir $@)/$(dir $<)
|
||
|
|
$(CXX) -fPIC $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) $(DEFS) $(SRA_DEF) $(HT2LIB_FLAGS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall $(INC) $(SEARCH_INC) \
|
||
|
|
-c -o $@ $<
|
||
|
|
|
||
|
|
.ht2lib-obj-debug-shared/%.o: %.cpp
|
||
|
|
@mkdir -p $(dir $@)/$(dir $<)
|
||
|
|
$(CXX) -fPIC $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) $(DEFS) $(SRA_DEF) $(HT2LIB_FLAGS) -DBOWTIE2 -Wall $(INC) $(SEARCH_INC) \
|
||
|
|
-c -o $@ $<
|
||
|
|
|
||
|
|
.ht2lib-obj-release-shared/%.o: %.cpp
|
||
|
|
@mkdir -p $(dir $@)/$(dir $<)
|
||
|
|
$(CXX) -fPIC $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) $(DEFS) $(SRA_DEF) $(HT2LIB_FLAGS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall $(INC) $(SEARCH_INC) \
|
||
|
|
-c -o $@ $<
|
||
|
|
|
||
|
|
#
|
||
|
|
# repeatexp
|
||
|
|
#
|
||
|
|
repeatexp:
|
||
|
|
g++ -o repeatexp repeatexp.cpp -I hisat2lib libhisat2lib.a
|
||
|
|
|
||
|
|
hisat2: ;
|
||
|
|
|
||
|
|
hisat2.bat:
|
||
|
|
echo "@echo off" > hisat2.bat
|
||
|
|
echo "perl %~dp0/hisat2 %*" >> hisat2.bat
|
||
|
|
|
||
|
|
hisat2-build.bat:
|
||
|
|
echo "@echo off" > hisat2-build.bat
|
||
|
|
echo "python %~dp0/hisat2-build %*" >> hisat2-build.bat
|
||
|
|
|
||
|
|
hisat2-inspect.bat:
|
||
|
|
echo "@echo off" > hisat2-inspect.bat
|
||
|
|
echo "python %~dp0/hisat2-inspect %*" >> hisat2-inspect.bat
|
||
|
|
|
||
|
|
|
||
|
|
.PHONY: hisat2-src
|
||
|
|
hisat2-src: $(SRC_PKG_LIST)
|
||
|
|
chmod a+x scripts/*.sh scripts/*.pl
|
||
|
|
mkdir .src.tmp
|
||
|
|
mkdir .src.tmp/hisat2-$(VERSION)
|
||
|
|
zip tmp.zip $(SRC_PKG_LIST)
|
||
|
|
mv tmp.zip .src.tmp/hisat2-$(VERSION)
|
||
|
|
cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
|
||
|
|
cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION)
|
||
|
|
cp .src.tmp/hisat2-$(VERSION)-source.zip .
|
||
|
|
rm -rf .src.tmp
|
||
|
|
|
||
|
|
.PHONY: hisat2-bin
|
||
|
|
hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)
|
||
|
|
chmod a+x scripts/*.sh scripts/*.pl
|
||
|
|
rm -rf .bin.tmp
|
||
|
|
mkdir .bin.tmp
|
||
|
|
mkdir .bin.tmp/hisat2-$(VERSION)
|
||
|
|
if [ -f hisat2.exe ] ; then \
|
||
|
|
zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \
|
||
|
|
else \
|
||
|
|
zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \
|
||
|
|
fi
|
||
|
|
mv tmp.zip .bin.tmp/hisat2-$(VERSION)
|
||
|
|
cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
|
||
|
|
cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION)
|
||
|
|
cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip .
|
||
|
|
rm -rf .bin.tmp
|
||
|
|
|
||
|
|
.PHONY: doc
|
||
|
|
doc: doc/manual.inc.html MANUAL
|
||
|
|
|
||
|
|
doc/manual.inc.html: MANUAL.markdown
|
||
|
|
pandoc -T "HISAT2 Manual" -o $@ \
|
||
|
|
--from markdown --to HTML --toc $^
|
||
|
|
perl -i -ne \
|
||
|
|
'$$w=0 if m|^</body>|;print if $$w;$$w=1 if m|^<body>|;' $@
|
||
|
|
|
||
|
|
MANUAL: MANUAL.markdown
|
||
|
|
perl doc/strip_markdown.pl < $^ > $@
|
||
|
|
|
||
|
|
.PHONY: clean
|
||
|
|
clean:
|
||
|
|
rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \
|
||
|
|
$(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) \
|
||
|
|
hisat2-src.zip hisat2-bin.zip
|
||
|
|
rm -f core.* .tmp.head
|
||
|
|
rm -rf *.dSYM
|
||
|
|
rm -rf .ht2lib-obj*
|
||
|
|
rm -f libhisat2lib*.a libhisat2lib*.so
|
||
|
|
|
||
|
|
|
||
|
|
.PHONY: push-doc
|
||
|
|
push-doc: doc/manual.inc.html
|
||
|
|
scp doc/*.*html doc/indexes.txt salz-dmz:/ccb/salz7-data/www/ccb.jhu.edu/html/software/hisat2/
|