diff options
Diffstat (limited to 'sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff')
| -rw-r--r-- | sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff | 533 |
1 files changed, 533 insertions, 0 deletions
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff new file mode 100644 index 000000000000..e6a8d60ec69c --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff @@ -0,0 +1,533 @@ +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 |