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Makefile.am
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Makefile.am
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# This file is part of abismal
#
# Copyright (C) 2018-2024: Andrew D. Smith and Guilherme de Sena Brandine
#
# Authors: Andrew D. Smith and Guilherme de Sena Brandine
#
# This 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.
#
# This software 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.
EXTRA_DIST = \
README.md \
LICENSE \
docs \
data/tRex1.fa \
data/md5sum.txt \
test_scripts/test_abismalidx.test \
test_scripts/test_simreads.test \
test_scripts/test_abismal.test \
test_scripts/test_simreads_pe.test \
test_scripts/test_abismal_pe.test \
test_scripts/test_simreads_pbat.test \
test_scripts/test_abismal_pbat.test \
test_scripts/test_simreads_rpbat.test \
test_scripts/test_abismal_rpbat.test \
test_scripts/test_abismal_threads.test
ACLOCAL_AMFLAGS = -I m4
SUBDIRS := src/smithlab_cpp
install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp, $(SUBDIRS))
AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
AM_CXXFLAGS = $(OPENMP_CXXFLAGS)
AM_CXXFLAGS += -Wall -Wextra -Wpedantic -Wno-unknown-attributes
if ENABLE_SHORT
AM_CXXFLAGS += -DENABLE_SHORT
endif
CXXFLAGS = -O3 -DNDEBUG # default has optimization on
noinst_LIBRARIES = libabismal.a
libabismal_a_SOURCES = \
src/abismal.cpp \
src/abismalidx.cpp \
src/AbismalIndex.cpp \
src/simreads.cpp
libabismal_a_SOURCES += \
src/abismal.hpp \
src/abismalidx.hpp \
src/simreads.hpp \
src/AbismalAlign.hpp \
src/AbismalIndex.hpp \
src/dna_four_bit_bisulfite.hpp \
src/popcnt.hpp \
src/abismal_cigar_utils.hpp \
src/bamxx/bamxx.hpp
LDADD = libabismal.a src/smithlab_cpp/libsmithlab_cpp.a
bin_PROGRAMS = abismal abismalidx simreads
abismal_SOURCES = src/abismal_main.cpp
abismalidx_SOURCES = src/abismalidx_main.cpp
simreads_SOURCES = src/simreads_main.cpp
TESTS = test_scripts/test_abismalidx.test \
test_scripts/test_simreads.test \
test_scripts/test_abismal.test \
test_scripts/test_simreads_pe.test \
test_scripts/test_abismal_pe.test \
test_scripts/test_simreads_pbat.test \
test_scripts/test_abismal_pbat.test \
test_scripts/test_simreads_rpbat.test \
test_scripts/test_abismal_rpbat.test \
test_scripts/test_abismal_threads.test
TEST_EXTENSIONS = .test
test_scripts/test_abismal.log: \
test_scripts/test_abismalidx.log \
test_scripts/test_simreads.log
test_scripts/test_abismal_pe.log: \
test_scripts/test_abismalidx.log \
test_scripts/test_simreads_pe.log
test_scripts/test_abismal_pbat.log: \
test_scripts/test_abismalidx.log \
test_scripts/test_simreads_pbat.log
test_scripts/test_abismal_rpbat.log: \
test_scripts/test_abismalidx.log \
test_scripts/test_simreads_rpbat.log
test_scripts/test_abismal_threads.log: \
test_scripts/test_abismalidx.log \
test_scripts/test_simreads.log \
test_scripts/test_simreads_pe.log \
test_scripts/test_simreads_pbat.log \
test_scripts/test_simreads_rpbat.log
CLEANFILES = \
tests/tRex1.idx \
tests/reads_1.fq \
tests/reads.mstats \
tests/reads.sam \
tests/reads_pe_1.fq \
tests/reads_pe_2.fq \
tests/reads_pe.mstats \
tests/reads_pe.sam \
tests/reads_pbat_pe_1.fq \
tests/reads_pbat_pe_2.fq \
tests/reads_pbat_pe.mstats \
tests/reads_pbat_pe.sam \
tests/reads_rpbat_pe_1.fq \
tests/reads_rpbat_pe_2.fq \
tests/reads_rpbat_pe.mstats \
tests/reads_rpbat_pe.sam