Commit 58bc4bd5 authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

New upstream version 2.00~a2-191115

parent d03de71d

Makefile

+3 −3
Original line number Diff line number Diff line
@@ -56,10 +56,10 @@ plink2: $(OBJ_NO_ZSTD) 
	$(MKDIR) -p bin

	$(CXX) $(ARCH32) $(OBJ_NO_ZSTD) -o bin/plink2 $(BLASFLAGS64) $(LDFLAGS)



# basic pgenlib_internal.h usage example; also needed for tests

pgen_compress: plink2_base.o pgenlib_internal.o pgen_compress.o

# basic pgenlib usage example; also needed for tests

pgen_compress: $(PGCOBJ)

	$(MKDIR) -p bin

	$(CXX) plink2_base.o pgenlib_internal.o pgen_compress.o \

	$(CXX) $(PGCOBJ) \

		-o bin/pgen_compress



.PHONY: install-strip install clean

Makefile.src

+6 −2
Original line number Diff line number Diff line
@@ -7,9 +7,9 @@ CXXWARN2 = ${CWARN2} -Wold-style-cast 


CSRC = SFMT.c libdeflate/lib/adler32.c libdeflate/lib/aligned_malloc.c libdeflate/lib/crc32.c libdeflate/lib/deflate_compress.c libdeflate/lib/deflate_decompress.c libdeflate/lib/gzip_compress.c libdeflate/lib/gzip_decompress.c libdeflate/lib/zlib_compress.c libdeflate/lib/zlib_decompress.c libdeflate/lib/x86/cpu_features.c



ZCSRC = zstd/lib/common/debug.c zstd/lib/common/entropy_common.c zstd/lib/common/zstd_common.c zstd/lib/common/error_private.c zstd/lib/common/xxhash.c zstd/lib/common/fse_decompress.c zstd/lib/common/pool.c zstd/lib/common/threading.c zstd/lib/compress/fse_compress.c zstd/lib/compress/hist.c zstd/lib/compress/huf_compress.c zstd/lib/compress/zstd_double_fast.c zstd/lib/compress/zstd_fast.c zstd/lib/compress/zstd_lazy.c zstd/lib/compress/zstd_ldm.c zstd/lib/compress/zstd_opt.c zstd/lib/compress/zstd_compress.c zstd/lib/compress/zstdmt_compress.c zstd/lib/decompress/huf_decompress.c zstd/lib/decompress/zstd_decompress.c zstd/lib/decompress/zstd_ddict.c zstd/lib/decompress/zstd_decompress_block.c

ZCSRC = zstd/lib/common/debug.c zstd/lib/common/entropy_common.c zstd/lib/common/zstd_common.c zstd/lib/common/error_private.c zstd/lib/common/xxhash.c zstd/lib/common/fse_decompress.c zstd/lib/common/pool.c zstd/lib/common/threading.c zstd/lib/compress/fse_compress.c zstd/lib/compress/hist.c zstd/lib/compress/huf_compress.c zstd/lib/compress/zstd_double_fast.c zstd/lib/compress/zstd_fast.c zstd/lib/compress/zstd_lazy.c zstd/lib/compress/zstd_ldm.c zstd/lib/compress/zstd_opt.c zstd/lib/compress/zstd_compress.c zstd/lib/compress/zstd_compress_literals.c zstd/lib/compress/zstd_compress_sequences.c zstd/lib/compress/zstdmt_compress.c zstd/lib/decompress/huf_decompress.c zstd/lib/decompress/zstd_decompress.c zstd/lib/decompress/zstd_ddict.c zstd/lib/decompress/zstd_decompress_block.c



CCSRC = plink2_base.cc pgenlib_internal.cc plink2.cc plink2_adjust.cc plink2_bgzf.cc plink2_cmdline.cc plink2_common.cc plink2_compress_stream.cc plink2_data.cc plink2_decompress.cc plink2_export.cc plink2_fasta.cc plink2_filter.cc plink2_glm.cc plink2_help.cc plink2_import.cc plink2_ld.cc plink2_matrix.cc plink2_matrix_calc.cc plink2_misc.cc plink2_psam.cc plink2_pvar.cc plink2_random.cc plink2_set.cc plink2_stats.cc plink2_string.cc plink2_text.cc plink2_thread.cc plink2_zstfile.cc

CCSRC = plink2_base.cc pgenlib_misc.cc pgenlib_read.cc pgenlib_write.cc plink2.cc plink2_adjust.cc plink2_bgzf.cc plink2_cmdline.cc plink2_common.cc plink2_compress_stream.cc plink2_data.cc plink2_decompress.cc plink2_export.cc plink2_fasta.cc plink2_filter.cc plink2_glm.cc plink2_help.cc plink2_import.cc plink2_ld.cc plink2_matrix.cc plink2_matrix_calc.cc plink2_misc.cc plink2_psam.cc plink2_pvar.cc plink2_random.cc plink2_set.cc plink2_stats.cc plink2_string.cc plink2_text.cc plink2_thread.cc plink2_zstfile.cc



OBJ_NO_ZSTD = $(CSRC:.c=.o) $(CCSRC:.cc=.o)

OBJ = $(CSRC:.c=.o) $(ZCSRC:.c=.o) $(CCSRC:.cc=.o)
@@ -26,5 +26,9 @@ CINCLUDE2 = -I../libdeflate -I../libdeflate/common 
ZSTD_INCLUDE = -Izstd/lib -Izstd/lib/common

ZSTD_INCLUDE2 = -I../zstd/lib -I../zstd/lib/common



PGCSRC = plink2_base.cc pgenlib_misc.cc pgenlib_read.cc pgenlib_write.cc pgen_compress.cc

PGCOBJ = $(PGCSRC:.c=.o)

PGCSRC2 = $(foreach fname,$(PGCSRC),../$(fname))



CLEAN = *.o libdeflate/lib/*.o libdeflate/lib/x86/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress

CLEAN3 = $(foreach expr,$(CLEAN),../$(expr))

Python/pgenlib.pyx

+169 −152

File changed.

Preview size limit exceeded, changes collapsed.

Python/setup.py

+2 −2
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ import numpy as np 


ext_modules = [

    Extension('pgenlib',

              sources = ['pgenlib.pyx', '../pgenlib_ffi_support.cc', '../pgenlib_internal.cc', '../plink2_base.cc'],

              sources = ['pgenlib.pyx', '../pgenlib_ffi_support.cc', '../pgenlib_misc.cc', '../pgenlib_read.cc', '../pgenlib_write.cc', '../plink2_base.cc'],

              language = "c++",

              # do not compile as c++11, since cython doesn't yet support

              # overload of uint32_t operator
@@ -21,6 +21,6 @@ ext_modules = [ 
    ]



setup(name = 'Pgenlib',

      version = '0.7',

      version = '0.71',

      description = "Wrapper for pgenlib's basic reader and writer.",

      ext_modules = cythonize(ext_modules))

build_dynamic/Makefile

+2 −2
Original line number Diff line number Diff line
@@ -150,8 +150,8 @@ plink2: $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc 
	g++ $(CPUCHECK_FLAGS) ../plink2_cpu.cc -c

	g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)



pgen_compress: ../plink2_base.cc ../pgenlib_internal.cc ../pgen_compress.cc

	g++ $(CXXFLAGS) ../plink2_base.cc ../pgenlib_internal.cc ../pgen_compress.cc -o pgen_compress

pgen_compress: $(PGCSRC2)

	g++ $(CXXFLAGS) $(PGCSRC2) -o pgen_compress



.PHONY: clean

clean: