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Makefile.am
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# This file is part of dnmtools
#
# Copyright (C) 2023-2024 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.
### ADS: the file md5sum.txt can be regenerated by running the tests
### with "make check" and then doing `md5sum tests/* > md5sum.txt`
### from the build directory.
ACLOCAL_AMFLAGS = -I m4
SUBDIRS := src/smithlab_cpp src/abismal
install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp src/abismal, $(SUBDIRS))
AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
AM_CXXFLAGS = $(OPENMP_CXXFLAGS)
CXXFLAGS = -Wall -Wextra -Wpedantic -Wno-unknown-attributes
CXXFLAGS += -O3 -DNDEBUG # default has optimization on
EXTRA_DIST = \
README.md \
code_of_conduct.md \
LICENSE \
docs/README.md \
docs/mkdocs.yml \
docs/content/abismal.md \
docs/content/allelic.md \
docs/content/amrfinder.md \
docs/content/amrtester.md \
docs/content/bsrate.md \
docs/content/cleanhp.md \
docs/content/counts.md \
docs/content/diff.md \
docs/content/dmr.md \
docs/content/entropy.md \
docs/content/fastlift.md \
docs/content/format.md \
docs/content/guessprotocol.md \
docs/content/hmr.md \
docs/content/hmr-rep.md \
docs/content/hypermr.md \
docs/content/index.md \
docs/content/lc.md \
docs/content/levels.md \
docs/content/liftfilter.md \
docs/content/merge-bsrate.md \
docs/content/merge.md \
docs/content/mlml.md \
docs/content/multistat.md \
docs/content/pmd.md \
docs/content/quickstart.md \
docs/content/radadjust.md \
docs/content/radmerge.md \
docs/content/radmeth.md \
docs/content/roi.md \
docs/content/selectsites.md \
docs/content/states.md \
docs/content/sym.md \
docs/content/uniq.md \
pipeline/config.yaml \
pipeline/runconfig.yaml \
pipeline/Snakefile \
data/md5sum.txt \
data/tRex1.fa \
data/tRex1_promoters.bed \
data/reads_1.fq.gz \
data/reads_2.fq.gz \
data/radmeth_test_table.txt \
data/radmeth_test_design.txt \
data/two_epialleles.states \
data/araTha1_simulated.counts.gz \
data/mlml_test_data.tgz \
data/pmd_test_data.counts.sym.gz \
test_scripts/test_abismalidx.test \
test_scripts/test_abismal.test \
test_scripts/test_format.test \
test_scripts/test_uniq.test \
test_scripts/test_bsrate.test \
test_scripts/test_counts.test \
test_scripts/test_levels.test \
test_scripts/test_sym.test \
test_scripts/test_hmr.test \
test_scripts/test_pmd.test \
test_scripts/test_roi.test \
test_scripts/test_selectsites.test \
test_scripts/test_radmeth.test \
test_scripts/test_states.test \
test_scripts/test_amrfinder.test \
test_scripts/test_hypermr.test \
test_scripts/test_diff.test \
test_scripts/test_xcounts.test \
test_scripts/test_unxcounts.test \
test_scripts/test_mlml.test
### ADS: Testing with `make check` can be a long process. Testing with
### `make check` is designed to work recursively. Modifying this
### behavior requires overriding build-in rules which generates
### warnings, probably for good reason. Defining a check-local only
### adds to functionality and does not remove the dependency that
### causes the recursion. The preferred alternative is to do `make`
### first and then `make check-TESTS` after. This will not do tests
### recursively.
TESTS = test_scripts/test_abismalidx.test \
test_scripts/test_abismal.test \
test_scripts/test_format.test \
test_scripts/test_uniq.test \
test_scripts/test_bsrate.test \
test_scripts/test_counts.test \
test_scripts/test_levels.test \
test_scripts/test_sym.test \
test_scripts/test_hmr.test \
test_scripts/test_pmd.test \
test_scripts/test_roi.test \
test_scripts/test_selectsites.test \
test_scripts/test_radmeth.test \
test_scripts/test_states.test \
test_scripts/test_amrfinder.test \
test_scripts/test_hypermr.test \
test_scripts/test_diff.test \
test_scripts/test_xcounts.test \
test_scripts/test_unxcounts.test \
test_scripts/test_mlml.test
TEST_EXTENSIONS = .test
test_scripts/test_abismal.log: test_scripts/test_abismalidx.log
test_scripts/test_format.log: test_scripts/test_abismal.log
test_scripts/test_uniq.log: test_scripts/test_format.log
test_scripts/test_bsrate.log: test_scripts/test_uniq.log
test_scripts/test_counts.log: test_scripts/test_uniq.log
test_scripts/test_states.log: test_scripts/test_uniq.log
test_scripts/test_levels.log: test_scripts/test_counts.log
test_scripts/test_selectsites.log: test_scripts/test_counts.log
test_scripts/test_sym.log: test_scripts/test_counts.log
test_scripts/test_hmr.log: test_scripts/test_sym.log
test_scripts/test_roi.log: test_scripts/test_sym.log
test_scripts/test_xcounts.log: test_scripts/test_counts.log
test_scripts/test_unxcounts.log: test_scripts/test_xcounts.log
noinst_LIBRARIES = libdnmtools.a
libdnmtools_a_SOURCES = \
src/common/dnmtools_gaussinv.cpp \
src/common/bam_record_utils.cpp \
src/common/counts_header.cpp \
src/common/xcounts_utils.cpp \
src/common/BetaBin.cpp \
src/common/EmissionDistribution.cpp \
src/common/Epiread.cpp \
src/common/EpireadStats.cpp \
src/common/LevelsCounter.cpp \
src/common/MSite.cpp \
src/common/Smoothing.cpp \
src/common/ThreeStateHMM.cpp \
src/common/TwoStateHMM.cpp \
src/common/TwoStateHMM_PMD.cpp \
src/common/bsutils.cpp \
src/common/numerical_utils.cpp \
src/common/dnmtools_utils.cpp
libdnmtools_a_SOURCES += \
src/bamxx/bamxx.hpp \
src/common/dnmtools_gaussinv.hpp \
src/common/bam_record_utils.hpp \
src/common/counts_header.hpp \
src/common/xcounts_utils.hpp \
src/common/BetaBin.hpp \
src/common/EmissionDistribution.hpp \
src/common/Epiread.hpp \
src/common/EpireadStats.hpp \
src/common/LevelsCounter.hpp \
src/common/MSite.hpp \
src/common/Smoothing.hpp \
src/common/ThreeStateHMM.hpp \
src/common/TwoStateHMM.hpp \
src/common/TwoStateHMM_PMD.hpp \
src/common/bsutils.hpp \
src/common/numerical_utils.hpp \
src/common/dnmtools_utils.hpp \
src/common/dnmt_error.hpp
# ADS: additional radmeth sources to help isolate the parts using GSL for
# optimization
libdnmtools_a_SOURCES += \
src/radmeth/radmeth_optimize.hpp \
src/radmeth/radmeth_model.hpp
LDADD = libdnmtools.a src/abismal/libabismal.a src/smithlab_cpp/libsmithlab_cpp.a
bin_PROGRAMS = dnmtools
dnmtools_SOURCES = src/dnmtools.cpp
dnmtools_SOURCES += src/analysis/pmd.cpp
dnmtools_SOURCES += src/analysis/methstates.cpp
dnmtools_SOURCES += src/analysis/bsrate.cpp
dnmtools_SOURCES += src/analysis/methentropy.cpp
dnmtools_SOURCES += src/analysis/methcounts.cpp
dnmtools_SOURCES += src/analysis/roimethstat.cpp
dnmtools_SOURCES += src/analysis/cpgbins.cpp
dnmtools_SOURCES += src/analysis/multimethstat.cpp
dnmtools_SOURCES += src/analysis/hmr.cpp
dnmtools_SOURCES += src/analysis/hmr-rep.cpp
dnmtools_SOURCES += src/analysis/levels.cpp
dnmtools_SOURCES += src/analysis/hypermr.cpp
dnmtools_SOURCES += src/analysis/metagene.cpp
dnmtools_SOURCES += src/utils/clean-hairpins.cpp
dnmtools_SOURCES += src/utils/guessprotocol.cpp
dnmtools_SOURCES += src/utils/uniq.cpp
dnmtools_SOURCES += src/utils/merge-bsrate.cpp
dnmtools_SOURCES += src/utils/format-reads.cpp
dnmtools_SOURCES += src/utils/lc-approx.cpp
dnmtools_SOURCES += src/utils/selectsites.cpp
dnmtools_SOURCES += src/utils/symmetric-cpgs.cpp
dnmtools_SOURCES += src/utils/merge-methcounts.cpp
dnmtools_SOURCES += src/utils/lift-filter.cpp
dnmtools_SOURCES += src/utils/fast-liftover.cpp
dnmtools_SOURCES += src/utils/covered.cpp
dnmtools_SOURCES += src/utils/recovered.cpp
dnmtools_SOURCES += src/utils/kmersites.cpp
dnmtools_SOURCES += src/utils/xcounts.cpp
dnmtools_SOURCES += src/utils/unxcounts.cpp
dnmtools_SOURCES += src/amrfinder/allelicmeth.cpp
dnmtools_SOURCES += src/amrfinder/amrfinder.cpp
dnmtools_SOURCES += src/amrfinder/amrtester.cpp
dnmtools_SOURCES += src/radmeth/dmr.cpp
dnmtools_SOURCES += src/radmeth/methdiff.cpp
dnmtools_SOURCES += src/radmeth/radmeth_optimize.cpp
dnmtools_SOURCES += src/radmeth/radmeth.cpp
dnmtools_SOURCES += src/radmeth/radmeth-adjust.cpp
dnmtools_SOURCES += src/radmeth/radmeth-merge.cpp
dnmtools_SOURCES += src/mlml/mlml.cpp
## ADS: these are the files output by the test scripts. They can be
## identified by doing:
##
## grep "^outfile" test_scripts/*.test
##
CLEANFILES = \
tests/reads.bsrate \
tests/reads.counts \
tests/reads.counts.sym \
tests/reads.fmt.sam \
tests/reads.fmt.srt.sam \
tests/reads.fmt.srt.uniq.sam \
tests/reads.hmr \
tests/reads.levels \
tests/reads.mstats \
tests/reads.sam \
tests/reads.ustats \
tests/tRex1.idx \
tests/tRex1_promoters.roi.bed \
tests/reads.counts.select \
tests/radmeth_test_output.txt \
tests/reads.epiread \
tests/two_epialleles.amr \
tests/araTha1_simulated.hypermr \
tests/methylome_ab.diff \
tests/methylome.pmd \
tests/reads.xcounts \
tests/reads.unxcounts \
tests/mlml.out