reinit the tree, so we can have metadata

7 files changed, 666 insertions, 0 deletions

diff --git a/sci-biology/snpfile/Manifest b/sci-biology/snpfile/Manifest
new file mode 100644
index 000000000000..d90be00d3b92
--- /dev/null
+++ b/sci-biology/snpfile/Manifest
@@ -0,0 +1,9 @@
+AUX snpfile-2.0.1-ax-boost.patch 973 SHA256 a698df5bd1bfe04f40cdec8275fe3fecfced9c0e8cb43939e9b70cf3fd25cb5a SHA512 cb517e30c06620de9d007261d238325daf48709ccd875d90c0cc99049dfd0ce80a506a3e9a97c786ac8329b1f1463a810407927cf17c1a25689b03f413417b94 WHIRLPOOL e91815cd15321f0bbb62d9e73a9ea3ed80027b284a7a81d42c3c49c249f0dc6e8d23419f6606d0e51083fbf53f200168f60c26d6bf09a59d3bff7a34397783e3
+AUX snpfile-2.0.1-gcc44.patch 387 SHA256 349c6594759f16da2602415ff217c37bb677e2508437497b508c91ab4668956a SHA512 ac66850cae2bbbad9e1a989772490eb23ea3958c233e0fe32b20ffb3d7b5f547ff9d045974170c3302e8ca6bbbe5a2055acad24bb80cc6a3c527c3164e3f0e84 WHIRLPOOL f72f1321fce7941981780246d8837d260097eaf71ad1f352ae2f7407971a6625f2f9fc319904bb95ceba190d9e51b63212901798f8bcd31114e7724eee6adc00
+AUX snpfile-2.0.1-gentoo.diff 20224 SHA256 b3275446db38b35999aa25bc2aeedec63b206baa8e4d339d256b7d25e425d1df SHA512 8628aa298b38376e439739c813ec87c80eb7c7f7874335e8f812eee05fab205ae900a00ec819021699fe835c2e9d38f880e9b391ccc4bfb46a8b91f028ed84ad WHIRLPOOL e96fda8d8f54ed912f48bfd539fa04a41c436f6e4b097f96baa6b1864dac2b55bc67a2ba309466c25b3bbc995d38517b7ee0a497107b9ea69cf8d2a2d982750e
+AUX snpfile-2.0.1-gold.patch 1066 SHA256 e9c256f07aacf233a5bf159fd25f536f91b650b425f9f8e39f83ac03741600e8 SHA512 81f2e5e91890e52cf40553ea70b12cdb09e5b8335303d72f6943e0058b62eb061eea4e52595c267de81af219f7b863025fb2aa7364d976101628b1f65ba27075 WHIRLPOOL 52465222846642807e2a721d8528dedb9cd5fdf3da1db8b793ed94d6ac3ef1fcab61621b4fceb0ee6eb5b6f99d89ac8bcaf584404bb1a8b4d064084e0535a69f
+DIST snpfile-2.0.1.tar.gz 171854 SHA256 71569e0dcd426447d1a5d215fb47615074a4c8d935cf70ef63c5f47a411b0b76 SHA512 e217e8b600d3ba7e2a8a0724d867bd9760572398f2e4e58625c1f74b0db9aa913db266da51fcfc05b90f3faf9eb6fbeb7bd988f105de013b51c24caa37c678c6 WHIRLPOOL c47391cde1a2fa8a93a1ab6ae0ee7e32519833fe08fd87ddc0ef0872e6bc9269ad0dc609b7c09a52248793dd0b31dcdc88a0528e966c4fa5845f4ae8c943ab9c
+EBUILD snpfile-2.0.1-r2.ebuild 886 SHA256 f8d6e6258b0174b926aa725f82d55aa7fb01a4b61e32f2eb5d2a4a1c9a32f0bc SHA512 7946475e80f92a1c76a4e92500cfad3f6eb4e0463014e07eb517f6a4ef0fb3ebff7143d18d22c887d970f186cc7a0847788d8b55e5b297d04820a9dfdb3475fa WHIRLPOOL a1e0f738ad79878d0fee33d6cd65a3a2ae86e011b777e56ab18e64c718970888284aecba4ffae382c2452e2b7da21bb2911aab473e3cb982d550898f61d0f330
+MISC ChangeLog 2593 SHA256 d47b1963a522cb0aa61fcac9c99bc19048532c6529acd17c35ec129bae26b3c9 SHA512 cdf29488256a34f777645873d76cc937d09358d9ed7595bf1ea88cea9d76d7afd0c8b5807bd2ffa45743b9cbeec3387b22f78c1c4615b6d7ffa427168ee8ff81 WHIRLPOOL de7ff1cae0892016453fc5585a026315e015cf7a77256e37f729f4ea13b8ffb306c3da397f9aeb265c02a72e4cb9f14983feb37ec696c0557f913aeb054408e7
+MISC ChangeLog-2015 1830 SHA256 4c163b37a8e5d54243edb64561dba7a7053b78a78c8292ce659abf802628daf3 SHA512 f1f9fd9c8afbf372df12122953fceae78c14e2835843ad48587cb2aff073cd1bdad5bc70e2b9ca4a74d4f6e63ae6acaf92fff815d411c25fef56596b3841df2e WHIRLPOOL 07f7460167f61aabf397d418c194ad02f0e00f23240a4e28b39aa3aec01524a9664fb78d3c6e90f76b2def9cfe12a639fe9460dee115be34972c156d845b9b90
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch b/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch
new file mode 100644
index 000000000000..f77b476f990d
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch
@@ -0,0 +1,35 @@
+Modernise autoconf code to use modern archive macros.
+
+--- a/configure.in
++++ b/configure.in
+@@ -1,7 +1,7 @@
+ AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk)
+ AM_INIT_AUTOMAKE
+ AC_CONFIG_MACRO_DIR([m4])
+-AM_CONFIG_HEADER(config.hh)
++AC_CONFIG_HEADERS([config.hh])
+ 
+ LT_INIT
+ AC_PROG_CXX
+@@ -14,18 +14,9 @@
+ fi
+ AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix])
+ 
+-AX_BOOST([1.33.1],,
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The Boost library was not found on this system.  We use this library
+-extensively, and cannot proceed without it.  You can obtain it from
+-<http://www.boost.org>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
++AX_BOOST_BASE([1.33.1])
++AX_BOOST_PROGRAM_OPTIONS
++AX_BOOST_SIGNALS
+ 
+ AC_OUTPUT([
+ 	Makefile
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch
new file mode 100644
index 000000000000..2b79c2492ede
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch
@@ -0,0 +1,12 @@
+diff -ur snpfile-2.0.1.orig/input_archive.hh snpfile-2.0.1/input_archive.hh
+--- snpfile-2.0.1.orig/input_archive.hh	2008-05-03 17:25:44.000000000 +0300
++++ snpfile-2.0.1/input_archive.hh	2009-07-26 21:26:10.000000000 +0300
+@@ -26,6 +26,8 @@
+ #ifndef INPUT_ARCHIVE_HH_INCLUDED
+ #define INPUT_ARCHIVE_HH_INCLUDED
+ 
++#include <stdint.h>
++
+ #include <string>
+ 
+ #include "archive_common.hh"
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..b2a8a6b630ce
--- /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
+
+--- a/Makefile.am
++++ b/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) $(BOOST_SIGNALS_LIB)
++
+--- a/configure.in
++++ b/configure.in
+@@ -1,10 +1,11 @@
+ AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk)
+ AM_INIT_AUTOMAKE
++AC_CONFIG_MACRO_DIR([m4])
+ AM_CONFIG_HEADER(config.hh)
+ 
++LT_INIT
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+-AC_PROG_RANLIB
+ 
+ if test "x$prefix" != xNONE; then
+    thePREFIX=$prefix
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch
new file mode 100644
index 000000000000..2211aa36c0ca
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch
@@ -0,0 +1,23 @@
+ Makefile.am |    4 ++--
+ 1 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 06fd733..5805c48 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -32,7 +32,7 @@ noinst_PROGRAMS += make_test_snpfile test_test_snpfile
+ noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \
+ 	matrix_benchmark_write matrix_benchmark_read
+ 
+-LDADD = $(top_builddir)/libsnpfile.la
++LDADD = $(top_builddir)/libsnpfile.la $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++
+ 
+ matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc
+ 
+@@ -88,5 +88,5 @@ libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix
+ 	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)
++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++
+ 
diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/snpfile/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild
new file mode 100644
index 000000000000..bbeb3111901f
--- /dev/null
+++ b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="A library and API for manipulating large SNP datasets"
+HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/"
+SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="static-libs"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-libs/boost:="
+DEPEND="
+	${RDEPEND}
+	>=sys-devel/autoconf-archive-2016.09.16"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-gcc44.patch
+	"${FILESDIR}"/${P}-gentoo.diff
+	"${FILESDIR}"/${P}-gold.patch
+	"${FILESDIR}"/${P}-ax-boost.patch
+)
+
+src_prepare() {
+	default
+	mv configure.{in,ac} || die
+	rm m4/ax_boost.m4 || die
+	eautoreconf
+}
+
+src_configure() {
+	econf $(use_enable static-libs static)
+}
+
+src_install() {
+	default
+
+	if ! use static-libs; then
+		find "${D}" -name '*.la' -delete || die
+	fi
+}