Makefile.am

# This file is part of preseq
#
# Copyright (C) 2018-2025: Andrew D. Smith
#
# Authors: Andrew D. Smith
#
# 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.

ACLOCAL_AMFLAGS = -I m4

AM_CPPFLAGS =
if ENABLE_HTSLIB
AM_CPPFLAGS += -I $(top_srcdir)/src/bamxx
endif

AM_CPPFLAGS += -Wall -Wextra -Wpedantic -Wno-unknown-attributes
if ENABLE_HTSLIB
AM_CPPFLAGS += -DHAVE_HTSLIB
endif

EXTRA_DIST = \
	README.md \
	LICENSE \
	preseqR \
	data \
	docs \
	tests/md5sum.txt \
	tests/data/lc_extrap_input.vals \
	tests/data/gc_extrap_input.bed \
	tests/data/c_curve_input.hist \
	tests/scripts/test_c_curve.test \
	tests/scripts/test_gc_extrap.test \
	tests/scripts/test_lc_extrap.test

TESTS = \
	tests/scripts/test_c_curve.test \
	tests/scripts/test_lc_extrap.test \
	tests/scripts/test_gc_extrap.test

TEST_EXTENSIONS = .test

bin_PROGRAMS = preseq

preseq_SOURCES = \
        src/preseq.cpp \
        src/common.hpp \
        src/common.cpp \
        src/c_curve.hpp \
        src/c_curve.cpp \
        src/gc_extrap.hpp \
        src/gc_extrap.cpp \
        src/lc_extrap.hpp \
        src/lc_extrap.cpp \
        src/bound_pop.hpp \
        src/bound_pop.cpp \
        src/pop_size.hpp \
        src/pop_size.cpp \
        src/continued_fraction.hpp \
        src/continued_fraction.cpp \
        src/load_data_for_complexity.hpp \
        src/load_data_for_complexity.cpp \
        src/Interval6.hpp \
        src/Interval6.cpp \
        src/moment_sequence.hpp \
        src/moment_sequence.cpp

if ENABLE_HTSLIB
preseq_SOURCES += \
	src/bamxx/bamxx.hpp \
	src/bam_record_utils.hpp \
        src/bam_record_utils.cpp
endif