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@@ -1,13 +1,126 @@ |
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diff --git a/Makefile.std b/Makefile.std |
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index 95b0940..630188a 100644 |
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index 95b0940..30206be 100644 |
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--- a/Makefile.std |
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+++ b/Makefile.std |
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@@ -22,7 +22,7 @@ endif |
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CFLAGS=-Wall -O2 |
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BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas |
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LINKFLAGS=-lm -lpthread |
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@@ -1,62 +1,22 @@ |
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# General-purpose Makefile for PLINK 1.90 |
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# |
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-# Compilation options: |
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-# Do not link to LAPACK NO_LAPACK |
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-# Leave blank after "=" to disable; put "= 1" to enable |
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-# (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h) |
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-NO_LAPACK = |
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- |
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- |
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-# should autodetect system |
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-SYS = UNIX |
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-ifdef SystemRoot |
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- SYS = WIN |
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-else |
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- UNAME := $(shell uname) |
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- ifeq ($(UNAME), Darwin) |
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- SYS = MAC |
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- endif |
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-endif |
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- |
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-CFLAGS=-Wall -O2 |
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-BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas |
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-LINKFLAGS=-lm -lpthread |
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-ZLIB=zlib-1.2.8/libz.so.1.2.8 |
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- |
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-ifeq ($(SYS), MAC) |
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- GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300) |
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- ifeq "$(GCC_GTEQ_43)" "1" |
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- CFLAGS=-Wall -O2 -flax-vector-conversions |
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- endif |
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- BLASFLAGS=-framework Accelerate |
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- LINKFLAGS= |
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- ZLIB=zlib-1.2.8/libz.1.2.8.dylib |
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-endif |
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- |
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-ifeq ($(SYS), WIN) |
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-# Note that, unlike the Linux and Mac build processes, this STATICALLY links |
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-# LAPACK, since we have not gotten around to trying dynamically-linked LAPACK |
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-# on Windows. |
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-# If you don't already have LAPACK built, you'll probably want to turn on |
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-# NO_LAPACK. |
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- BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a |
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- LINKFLAGS=-lm -static-libgcc |
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- ZLIB=zlib-1.2.8/libz.a |
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-endif |
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- |
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-ifdef NO_LAPACK |
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- BLASFLAGS= |
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-endif |
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+# CFLAGS=-Wall -O2 |
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+# BLASFLAGS=-lblas -llapack -latlas |
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+LINKFLAGS=-lm -lpthread -lopenblas -llapack -latlas -lstdc++ |
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+ZLIB=-lz |
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ifeq ($(SYS), MAC) |
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GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300) |
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SRC = plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c |
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+OBJ = plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o |
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+ |
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# In the likely event that you are concurrently using PLINK 1.07, we suggest |
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# either renaming that binary to "plink1" or this one to "plink2". |
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-plink: $(SRC) |
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- g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) |
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+# plink: $(SRC) |
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+# g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) |
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-plinkw: $(SRC) |
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+plink: $(SRC) |
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g++ $(CFLAGS) $(SRC) -c |
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- gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) |
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+ gfortran $(OBJ) -o plink2 $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) |
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+ # gfortran $^ -o plink2 -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) |
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diff --git a/dose2plink.c b/dose2plink.c |
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index dc1f33a..ca2d31c 100644 |
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--- a/dose2plink.c |
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+++ b/dose2plink.c |
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@@ -96,7 +96,7 @@ |
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#endif |
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#endif |
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-#include "zlib-1.2.8/zlib.h" |
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+#include "zlib.h" |
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#ifdef __APPLE__ |
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#include <sys/sysctl.h> |
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diff --git a/pigz.c b/pigz.c |
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index 6605925..3f4ca54 100644 |
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--- a/pigz.c |
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+++ b/pigz.c |
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@@ -303,7 +303,7 @@ |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <windows.h> |
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-#include "zlib-1.2.8/zlib.h" |
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+#include "zlib.h" |
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void pigz_init(uint32_t setprocs) { |
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return; |
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@@ -383,7 +383,7 @@ void parallel_compress(char* out_fname, uint32_t do_append, uint32_t(* emitn)(ui |
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# include <sys/pstat.h> |
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#endif |
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-#include "zlib-1.2.8/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */ |
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+#include "zlib.h" /* deflateInit2(), deflateReset(), deflate(), */ |
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/* deflateEnd(), deflateSetDictionary(), crc32(), |
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inflateBackInit(), inflateBack(), inflateBackEnd(), |
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Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY, |
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diff --git a/plink_common.h b/plink_common.h |
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index 5dd77e8..4da9371 100644 |
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--- a/plink_common.h |
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+++ b/plink_common.h |
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@@ -139,7 +139,7 @@ |
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#endif // __LP64__ |
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-#include "zlib-1.2.8/zlib.h" |
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+#include "zlib.h" |
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#include "SFMT.h" |
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// 64MB of non-workspace memory guaranteed for now |