| Fixing as-needed issues, provide shared libs |
| |
| https://bugs.gentoo.org/show_bug.cgi?id=294971 |
| |
| --- Makefile.am |
| +++ Makefile.am |
| @@ -1,440 +1,92 @@ |
| ACLOCAL_AMFLAGS = -I m4 |
| |
| -AM_CXXFLAGS = |
| -AM_CXXFLAGS += -Wall |
| -AM_CXXFLAGS += $(BOOST_CPPFLAGS) |
| +AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS) |
| +SUFFIXES = .cc |
| |
| - |
| -# for testing |
| -AM_CXXFLAGS += -g -O2 #-lefence |
| - |
| -# for profiling |
| -#CXXFLAGS += -O3 -g -pg |
| -#AM_CXXFLAGS += -O3 -g -pg |
| - |
| -# for production |
| -#CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG |
| -#AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG |
| - |
| -# for coverage testing |
| -#CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations |
| -#AM_CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations |
| - |
| - |
| -lib_LIBRARIES = libsnpfile.a |
| +lib_LTLIBRARIES = libsnpfile.la |
| |
| noinst_PROGRAMS = |
| -TESTS = |
| -EXTRA_DIST = |
| -bin_PROGRAMS = |
| |
| # conversion tools |
| -bin_PROGRAMS += text2snpfile |
| -bin_PROGRAMS += snpfile2text |
| -bin_PROGRAMS += snpfile2fastPHASE |
| -bin_PROGRAMS += fastPHASE2snpfile |
| -bin_PROGRAMS += snpfile2haploview |
| -bin_PROGRAMS += beagle_phase_snpfile |
| +bin_PROGRAMS = text2snpfile snpfile2text snpfile2fastPHASE fastPHASE2snpfile \ |
| + snpfile2haploview beagle_phase_snpfile |
| |
| # data extraction tools |
| -bin_PROGRAMS += snpfile_genotype_count |
| -bin_PROGRAMS += snpfile_phenotypes |
| -bin_PROGRAMS += snpfile_markers |
| - |
| -bin_PROGRAMS += snpfile_metadata_info |
| -bin_PROGRAMS += snpfile_set_metadata |
| -bin_PROGRAMS += snpfile_get_metadata |
| +bin_PROGRAMS += snpfile_genotype_count snpfile_phenotypes snpfile_markers |
| + |
| +bin_PROGRAMS += snpfile_metadata_info snpfile_set_metadata snpfile_get_metadata |
| |
| # other tools |
| noinst_PROGRAMS += snpfile_split_on_column |
| |
| # tests |
| -noinst_PROGRAMS += matrix_test |
| -TESTS += matrix_test |
| -noinst_PROGRAMS += file_test |
| -TESTS += file_test |
| -noinst_PROGRAMS += file_matrix_test |
| -TESTS += file_matrix_test |
| -noinst_PROGRAMS += readonly_matrix_test |
| -TESTS += readonly_matrix_test |
| -noinst_PROGRAMS += archives_test |
| -TESTS += archives_test |
| -noinst_PROGRAMS += metadata_access_test |
| -TESTS += metadata_access_test |
| -noinst_PROGRAMS += metadata_types_test |
| -TESTS += metadata_types_test |
| -noinst_PROGRAMS += iterators_test |
| -TESTS += iterators_test |
| -noinst_PROGRAMS += tabulate_test |
| -TESTS += tabulate_test |
| -noinst_PROGRAMS += metadata_filtering_test |
| -TESTS += metadata_filtering_test |
| +TESTS = matrix_test file_test file_matrix_test readonly_matrix_test archives_test \ |
| + metadata_access_test metadata_types_test iterators_test tabulate_test metadata_filtering_test |
| + |
| +noinst_PROGRAMS += $(TESTS) |
| |
| #Utils for testing across different machines |
| -noinst_PROGRAMS += make_test_snpfile |
| -noinst_PROGRAMS += test_test_snpfile |
| +noinst_PROGRAMS += make_test_snpfile test_test_snpfile |
| |
| # other experiments... |
| -noinst_PROGRAMS += row_metadata_experiment |
| -noinst_PROGRAMS += metadata_cache_prototype |
| -noinst_PROGRAMS += matrix_benchmark |
| -noinst_PROGRAMS += matrix_benchmark_write |
| -noinst_PROGRAMS += matrix_benchmark_read |
| - |
| - |
| - |
| -matrix_test_LDADD = |
| -matrix_test_LDADD += $(BOOST_SIGNALS_LIB) |
| -matrix_test_SOURCES = |
| -matrix_test_SOURCES += test_util.hh test_util.cc |
| -matrix_test_SOURCES += matrix.hh matrix.cc |
| -matrix_test_SOURCES += array_matrix.hh array_matrix.cc |
| -matrix_test_SOURCES += file_matrix.hh file_matrix.cc |
| -matrix_test_SOURCES += input_archive.hh |
| -matrix_test_SOURCES += output_archive.hh |
| -matrix_test_SOURCES += metadata.hh metadata.cc |
| -matrix_test_SOURCES += snpfile.hh snpfile.cc |
| -matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -matrix_test_SOURCES += matrix_test.cc |
| - |
| - |
| -file_test_LDADD = |
| -file_test_LDADD += $(BOOST_SIGNALS_LIB) |
| -file_test_SOURCES = |
| -file_test_SOURCES += test_util.hh test_util.cc |
| -file_test_SOURCES += metadata.hh metadata.cc |
| -file_test_SOURCES += snpfile.hh snpfile.cc |
| -file_test_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -file_test_SOURCES += file_test.cc |
| -file_test_SOURCES += metadata_access.hh |
| -file_test_SOURCES += input_archive.hh |
| -file_test_SOURCES += output_archive.hh |
| - |
| -file_matrix_test_LDADD = |
| -file_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) |
| -file_matrix_test_SOURCES = |
| -file_matrix_test_SOURCES += test_util.hh test_util.cc |
| -file_matrix_test_SOURCES += file_matrix.hh file_matrix.cc |
| -file_matrix_test_SOURCES += matrix.hh matrix.cc |
| -file_matrix_test_SOURCES += input_archive.hh |
| -file_matrix_test_SOURCES += output_archive.hh |
| -file_matrix_test_SOURCES += metadata.hh metadata.cc |
| -file_matrix_test_SOURCES += snpfile.hh snpfile.cc |
| -file_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -file_matrix_test_SOURCES += file_matrix_test.cc |
| - |
| - |
| -readonly_matrix_test_LDADD = |
| -readonly_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) |
| -readonly_matrix_test_SOURCES = |
| -readonly_matrix_test_SOURCES += test_util.hh test_util.cc |
| -readonly_matrix_test_SOURCES += array_matrix.hh array_matrix.cc |
| -readonly_matrix_test_SOURCES += file_matrix.hh file_matrix.cc |
| -readonly_matrix_test_SOURCES += matrix.hh matrix.cc |
| -readonly_matrix_test_SOURCES += input_archive.hh |
| -readonly_matrix_test_SOURCES += output_archive.hh |
| -readonly_matrix_test_SOURCES += metadata.hh metadata.cc |
| -readonly_matrix_test_SOURCES += snpfile.hh snpfile.cc |
| -readonly_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -readonly_matrix_test_SOURCES += readonly_matrix_test.cc |
| - |
| - |
| -archives_test_SOURCES = |
| -archives_test_SOURCES += input_archive.hh |
| -archives_test_SOURCES += output_archive.hh |
| -archives_test_SOURCES += archives_test.cc |
| - |
| - |
| -metadata_access_test_LDADD = |
| -metadata_access_test_LDADD += $(BOOST_SIGNALS_LIB) |
| -metadata_access_test_SOURCES = |
| -metadata_access_test_SOURCES += test_util.hh test_util.cc |
| -metadata_access_test_SOURCES += metadata.hh metadata.cc |
| -metadata_access_test_SOURCES += snpfile.hh snpfile.cc |
| -metadata_access_test_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -metadata_access_test_SOURCES += input_archive.hh |
| -metadata_access_test_SOURCES += output_archive.hh |
| -metadata_access_test_SOURCES += serialization_trait.hh |
| -metadata_access_test_SOURCES += metadata_access_test.cc |
| - |
| - |
| -metadata_types_test_LDADD = |
| -metadata_types_test_LDADD += $(BOOST_SIGNALS_LIB) |
| -metadata_types_test_SOURCES = |
| -metadata_types_test_SOURCES += test_util.hh test_util.cc |
| -metadata_types_test_SOURCES += metadata.hh metadata.cc |
| -metadata_types_test_SOURCES += snpfile.hh snpfile.cc |
| -metadata_types_test_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -metadata_types_test_SOURCES += input_archive.hh |
| -metadata_types_test_SOURCES += output_archive.hh |
| -metadata_types_test_SOURCES += serialization_trait.hh |
| -metadata_types_test_SOURCES += metadata_types_test.cc |
| - |
| - |
| -iterators_test_SOURCES = |
| -iterators_test_SOURCES += iterators.hh |
| -iterators_test_SOURCES += array_matrix.hh array_matrix.cc |
| -iterators_test_SOURCES += matrix.hh matrix.cc |
| -iterators_test_SOURCES += iterators_test.cc |
| - |
| - |
| -tabulate_test_SOURCES = |
| -tabulate_test_SOURCES += tabulate.hh |
| -tabulate_test_SOURCES += array_matrix.hh array_matrix.cc |
| -tabulate_test_SOURCES += matrix.hh matrix.cc |
| -tabulate_test_SOURCES += tabulate_test.cc |
| - |
| - |
| -metadata_filtering_test_SOURCES = |
| -metadata_filtering_test_SOURCES += matrix.hh matrix.cc |
| -metadata_filtering_test_SOURCES += array_matrix.hh array_matrix.cc |
| -metadata_filtering_test_SOURCES += metadata_filtering.hh |
| -metadata_filtering_test_SOURCES += metadata_filtering_test.cc |
| - |
| - |
| -make_test_snpfile_LDADD = |
| -make_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) |
| -make_test_snpfile_SOURCES = |
| -make_test_snpfile_SOURCES += metadata.hh metadata.cc |
| -make_test_snpfile_SOURCES += snpfile.hh snpfile.cc |
| -make_test_snpfile_SOURCES += matrix.hh matrix.cc |
| -make_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc |
| -make_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -make_test_snpfile_SOURCES += input_archive.hh |
| -make_test_snpfile_SOURCES += output_archive.hh |
| -make_test_snpfile_SOURCES += make_test_snpfile.cc |
| - |
| - |
| -test_test_snpfile_LDADD = |
| -test_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) |
| -test_test_snpfile_SOURCES = |
| -test_test_snpfile_SOURCES += metadata.hh metadata.cc |
| -test_test_snpfile_SOURCES += snpfile.hh snpfile.cc |
| -test_test_snpfile_SOURCES += matrix.hh matrix.cc |
| -test_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc |
| -test_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -test_test_snpfile_SOURCES += input_archive.hh |
| -test_test_snpfile_SOURCES += output_archive.hh |
| -test_test_snpfile_SOURCES += test_test_snpfile.cc |
| - |
| - |
| -row_metadata_experiment_LDADD = |
| -row_metadata_experiment_LDADD += $(BOOST_SIGNALS_LIB) |
| -row_metadata_experiment_SOURCES = |
| -row_metadata_experiment_SOURCES += matrix.hh matrix.cc |
| -row_metadata_experiment_SOURCES += array_matrix.hh array_matrix.cc |
| -row_metadata_experiment_SOURCES += file_matrix.hh file_matrix.cc |
| -row_metadata_experiment_SOURCES += input_archive.hh |
| -row_metadata_experiment_SOURCES += output_archive.hh |
| -row_metadata_experiment_SOURCES += metadata.hh metadata.cc |
| -row_metadata_experiment_SOURCES += snpfile.hh snpfile.cc |
| -row_metadata_experiment_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -row_metadata_experiment_SOURCES += test_util.hh test_util.cc |
| -row_metadata_experiment_SOURCES += row_metadata_experiment.cc |
| - |
| - |
| -metadata_cache_prototype_SOURCES = |
| -metadata_cache_prototype_SOURCES += metadata_cache_prototype.cc |
| -metadata_cache_prototype_LDFLAGS = |
| -metadata_cache_prototype_LDFLAGS += -L. |
| -metadata_cache_prototype_LDADD = |
| -metadata_cache_prototype_LDADD += $(BOOST_SIGNALS_LIB) |
| -metadata_cache_prototype_LDADD += -lsnpfile |
| - |
| - |
| -matrix_benchmark_LDADD = |
| -matrix_benchmark_LDADD += $(BOOST_SIGNALS_LIB) |
| -matrix_benchmark_SOURCES = |
| -matrix_benchmark_SOURCES += test_util.hh test_util.cc |
| -matrix_benchmark_SOURCES += file_matrix.hh file_matrix.cc |
| -matrix_benchmark_SOURCES += array_matrix.hh array_matrix.cc |
| -matrix_benchmark_SOURCES += matrix.hh matrix.cc |
| -matrix_benchmark_SOURCES += input_archive.hh |
| -matrix_benchmark_SOURCES += output_archive.hh |
| -matrix_benchmark_SOURCES += metadata.hh metadata.cc |
| -matrix_benchmark_SOURCES += snpfile.hh snpfile.cc |
| -matrix_benchmark_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -matrix_benchmark_SOURCES += timing.hh timing.cc |
| -matrix_benchmark_SOURCES += matrix_benchmark.cc |
| - |
| - |
| -matrix_benchmark_write_LDADD = |
| -matrix_benchmark_write_LDADD += $(BOOST_SIGNALS_LIB) |
| -matrix_benchmark_write_SOURCES = |
| -matrix_benchmark_write_SOURCES += file_matrix.hh file_matrix.cc |
| -matrix_benchmark_write_SOURCES += matrix.hh matrix.cc |
| -matrix_benchmark_write_SOURCES += input_archive.hh |
| -matrix_benchmark_write_SOURCES += output_archive.hh |
| -matrix_benchmark_write_SOURCES += metadata.hh metadata.cc |
| -matrix_benchmark_write_SOURCES += snpfile.hh snpfile.cc |
| -matrix_benchmark_write_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -matrix_benchmark_write_SOURCES += timing.hh timing.cc |
| -matrix_benchmark_write_SOURCES += matrix_benchmark_write.cc |
| - |
| - |
| -matrix_benchmark_read_LDADD = |
| -matrix_benchmark_read_LDADD += $(BOOST_SIGNALS_LIB) |
| -matrix_benchmark_read_SOURCES = |
| -matrix_benchmark_read_SOURCES += file_matrix.hh file_matrix.cc |
| -matrix_benchmark_read_SOURCES += matrix.hh matrix.cc |
| -matrix_benchmark_read_SOURCES += input_archive.hh |
| -matrix_benchmark_read_SOURCES += output_archive.hh |
| -matrix_benchmark_read_SOURCES += metadata.hh metadata.cc |
| -matrix_benchmark_read_SOURCES += snpfile.hh snpfile.cc |
| -matrix_benchmark_read_SOURCES += byte_order_handler.hh byte_order_handler.cc |
| -matrix_benchmark_read_SOURCES += timing.hh timing.cc |
| -matrix_benchmark_read_SOURCES += matrix_benchmark_read.cc |
| +noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ |
| + matrix_benchmark_write matrix_benchmark_read |
| + |
| +LDADD = $(top_builddir)/libsnpfile.la |
| + |
| +matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc |
| + |
| +file_test_SOURCES = test_util.hh test_util.cc file_test.cc metadata_access.hh input_archive.hh \ |
| + output_archive.hh |
| + |
| +file_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ |
| + file_matrix_test.cc |
| + |
| +readonly_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ |
| + readonly_matrix_test.cc |
| |
| +archives_test_SOURCES = input_archive.hh output_archive.hh archives_test.cc |
| + |
| +metadata_access_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ |
| + serialization_trait.hh metadata_access_test.cc |
| + |
| +metadata_types_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ |
| + serialization_trait.hh metadata_types_test.cc |
| + |
| +iterators_test_SOURCES = iterators.hh iterators_test.cc |
| + |
| +tabulate_test_SOURCES = tabulate.hh tabulate_test.cc |
| + |
| +metadata_filtering_test_SOURCES = metadata_filtering.hh metadata_filtering_test.cc |
| + |
| +make_test_snpfile_SOURCES = input_archive.hh output_archive.hh make_test_snpfile.cc |
| + |
| +test_test_snpfile_SOURCES = input_archive.hh output_archive.hh test_test_snpfile.cc |
| + |
| +row_metadata_experiment_SOURCES = input_archive.hh output_archive.hh test_util.hh test_util.cc \ |
| + row_metadata_experiment.cc |
| + |
| +matrix_benchmark_SOURCES = test_util.hh test_util.cc input_archive.hh \ |
| + output_archive.hh timing.hh timing.cc matrix_benchmark.cc |
| + |
| +matrix_benchmark_write_SOURCES = input_archive.hh output_archive.hh \ |
| + timing.hh timing.cc matrix_benchmark_write.cc |
| + |
| +matrix_benchmark_read_SOURCES = input_archive.hh output_archive.hh \ |
| + timing.hh timing.cc matrix_benchmark_read.cc |
| + |
| +snpfile_genotype_count_SOURCES = genotype_count.cc |
| |
| snpfileincludedir = $(includedir)/snpfile |
| -snpfileinclude_HEADERS = |
| -snpfileinclude_HEADERS += common.hh |
| -snpfileinclude_HEADERS += matrix.hh |
| -snpfileinclude_HEADERS += file_matrix.hh |
| -snpfileinclude_HEADERS += array_matrix.hh |
| -snpfileinclude_HEADERS += byte_order_handler.hh |
| -snpfileinclude_HEADERS += metadata.hh |
| -snpfileinclude_HEADERS += metadata_access.hh |
| -snpfileinclude_HEADERS += archive_common.hh |
| -snpfileinclude_HEADERS += archives.hh |
| -snpfileinclude_HEADERS += input_archive.hh |
| -snpfileinclude_HEADERS += output_archive.hh |
| -snpfileinclude_HEADERS += snpfile.hh |
| -snpfileinclude_HEADERS += serialization_trait.hh |
| -snpfileinclude_HEADERS += type_trait.hh |
| -snpfileinclude_HEADERS += iterators.hh |
| -snpfileinclude_HEADERS += tabulate.hh |
| - |
| -libsnpfile_a_SOURCES = |
| -libsnpfile_a_SOURCES += common.hh |
| -libsnpfile_a_SOURCES += matrix.hh matrix.cc |
| -libsnpfile_a_SOURCES += file_matrix.hh file_matrix.cc |
| -libsnpfile_a_SOURCES += array_matrix.cc array_matrix.hh |
| -libsnpfile_a_SOURCES += byte_order_handler.cc byte_order_handler.hh |
| -libsnpfile_a_SOURCES += metadata.hh metadata.cc metadata_access.hh |
| -libsnpfile_a_SOURCES += archive_common.hh |
| -libsnpfile_a_SOURCES += archives.hh |
| -libsnpfile_a_SOURCES += input_archive.hh |
| -libsnpfile_a_SOURCES += output_archive.hh |
| -libsnpfile_a_SOURCES += snpfile.hh snpfile.cc |
| -libsnpfile_a_SOURCES += serialization_trait.hh |
| -libsnpfile_a_SOURCES += type_trait.hh |
| - |
| -text2snpfile_SOURCES = |
| -text2snpfile_SOURCES += text2snpfile.cc |
| -text2snpfile_LDFLAGS = |
| -text2snpfile_LDFLAGS += -L. |
| -text2snpfile_LDADD = |
| -text2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -text2snpfile_LDADD += $(BOOST_SIGNALS_LIB) |
| -text2snpfile_LDADD += -lsnpfile |
| - |
| -snpfile2text_SOURCES = |
| -snpfile2text_SOURCES += snpfile2text.cc |
| -snpfile2text_LDFLAGS = |
| -snpfile2text_LDFLAGS += -L. |
| -snpfile2text_LDADD = |
| -snpfile2text_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile2text_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile2text_LDADD += -lsnpfile |
| - |
| - |
| -snpfile2fastPHASE_SOURCES = |
| -snpfile2fastPHASE_SOURCES += snpfile2fastPHASE.cc |
| -snpfile2fastPHASE_LDFLAGS = |
| -snpfile2fastPHASE_LDFLAGS += -L. |
| -snpfile2fastPHASE_LDADD = |
| -snpfile2fastPHASE_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile2fastPHASE_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile2fastPHASE_LDADD += -lsnpfile |
| - |
| -fastPHASE2snpfile_SOURCES = |
| -fastPHASE2snpfile_SOURCES += fastPHASE2snpfile.cc |
| -fastPHASE2snpfile_LDFLAGS = |
| -fastPHASE2snpfile_LDFLAGS += -L. |
| -fastPHASE2snpfile_LDADD = |
| -fastPHASE2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -fastPHASE2snpfile_LDADD += $(BOOST_SIGNALS_LIB) |
| -fastPHASE2snpfile_LDADD += -lsnpfile |
| - |
| - |
| -snpfile2haploview_SOURCES = |
| -snpfile2haploview_SOURCES += snpfile2haploview.cc |
| -snpfile2haploview_LDFLAGS = |
| -snpfile2haploview_LDFLAGS += -L. |
| -snpfile2haploview_LDADD = |
| -snpfile2haploview_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile2haploview_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile2haploview_LDADD += -lsnpfile |
| - |
| - |
| -beagle_phase_snpfile_SOURCES = |
| -beagle_phase_snpfile_SOURCES += beagle_phase_snpfile.cc |
| -beagle_phase_snpfile_LDFLAGS = |
| -beagle_phase_snpfile_LDFLAGS += -L. |
| -beagle_phase_snpfile_LDADD = |
| -beagle_phase_snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -beagle_phase_snpfile_LDADD += $(BOOST_SIGNALS_LIB) |
| -beagle_phase_snpfile_LDADD += -lsnpfile |
| - |
| -snpfile_genotype_count_SOURCES = |
| -snpfile_genotype_count_SOURCES += genotype_count.cc |
| -snpfile_genotype_count_LDFLAGS = |
| -snpfile_genotype_count_LDFLAGS += -L. |
| -snpfile_genotype_count_LDADD = |
| -snpfile_genotype_count_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile_genotype_count_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile_genotype_count_LDADD += -lsnpfile |
| - |
| -snpfile_phenotypes_SOURCES = |
| -snpfile_phenotypes_SOURCES += snpfile_phenotypes.cc |
| -snpfile_phenotypes_LDFLAGS = |
| -snpfile_phenotypes_LDFLAGS += -L. |
| -snpfile_phenotypes_LDADD = |
| -snpfile_phenotypes_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile_phenotypes_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile_phenotypes_LDADD += -lsnpfile |
| - |
| -snpfile_markers_SOURCES = |
| -snpfile_markers_SOURCES += snpfile_markers.cc |
| -snpfile_markers_LDFLAGS = |
| -snpfile_markers_LDFLAGS += -L. |
| -snpfile_markers_LDADD = |
| -snpfile_markers_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile_markers_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile_markers_LDADD += -lsnpfile |
| - |
| -snpfile_metadata_info_SOURCES = |
| -snpfile_metadata_info_SOURCES += snpfile_metadata_info.cc |
| -snpfile_metadata_info_LDFLAGS = |
| -snpfile_metadata_info_LDFLAGS += -L. |
| -snpfile_metadata_info_LDADD = |
| -snpfile_metadata_info_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile_metadata_info_LDADD += -lsnpfile |
| - |
| -snpfile_set_metadata_SOURCES = |
| -snpfile_set_metadata_SOURCES += snpfile_set_metadata.cc |
| -snpfile_set_metadata_LDFLAGS = |
| -snpfile_set_metadata_LDFLAGS += -L. |
| -snpfile_set_metadata_LDADD = |
| -snpfile_set_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile_set_metadata_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile_set_metadata_LDADD += -lsnpfile |
| - |
| -snpfile_get_metadata_SOURCES = |
| -snpfile_get_metadata_SOURCES += snpfile_get_metadata.cc |
| -snpfile_get_metadata_LDFLAGS = |
| -snpfile_get_metadata_LDFLAGS += -L. |
| -snpfile_get_metadata_LDADD = |
| -snpfile_get_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile_get_metadata_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile_get_metadata_LDADD += -lsnpfile |
| - |
| -snpfile_split_on_column_SOURCES = |
| -snpfile_split_on_column_SOURCES += snpfile_split_on_column.cc |
| -snpfile_split_on_column_LDFLAGS = |
| -snpfile_split_on_column_LDFLAGS += -L. |
| -snpfile_split_on_column_LDADD = |
| -snpfile_split_on_column_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
| -snpfile_split_on_column_LDADD += $(BOOST_SIGNALS_LIB) |
| -snpfile_split_on_column_LDADD += -lsnpfile |
| +snpfileinclude_HEADERS = common.hh matrix.hh file_matrix.hh array_matrix.hh \ |
| + byte_order_handler.hh metadata.hh metadata_access.hh archive_common.hh \ |
| + archives.hh input_archive.hh output_archive.hh snpfile.hh serialization_trait.hh \ |
| + type_trait.hh iterators.hh tabulate.hh |
| + |
| +libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix.cc \ |
| + array_matrix.cc array_matrix.hh byte_order_handler.cc byte_order_handler.hh \ |
| + metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ |
| + input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ |
| + type_trait.hh |
| +libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) |
| + |
| --- configure.in |
| +++ configure.in |
| @@ -1,10 +1,11 @@ |
| AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk) |
| AM_INIT_AUTOMAKE |
| +AC_CONFIG_MACRO_DIR([m4]) |
| AM_CONFIG_HEADER(config.hh) |
| |
| +LT_INIT |
| AC_PROG_CXX |
| AC_PROG_INSTALL |
| -AC_PROG_RANLIB |
| |
| if test "x$prefix" != xNONE; then |
| thePREFIX=$prefix |
