Added git version of plink-ng

1 files changed, 129 insertions, 0 deletions

diff --git a/plink-ng-Makefile-zlib-git.patch b/plink-ng-Makefile-zlib-git.patch
new file mode 100644
index 0000000..79986b8
--- /dev/null
+++ b/plink-ng-Makefile-zlib-git.patch
@@ -0,0 +1,129 @@
+diff --git a/Makefile.std b/Makefile.std
+index e204486..ca65bd3 100644
+--- a/Makefile.std
++++ b/Makefile.std
+@@ -1,64 +1,23 @@
+ # General-purpose Makefile for PLINK 1.90
+ #
+-# Compilation options:
+-#   Do not link to LAPACK                    NO_LAPACK
+ 
+-# Leave blank after "=" to disable; put "= 1" to enable
+-# (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h)
+-NO_LAPACK =
++# CFLAGS=-Wall -O2
++# BLASFLAGS=-lblas -llapack -latlas
++LINKFLAGS=-lm -lpthread -lopenblas -llapack -latlas -lstdc++
++ZLIB=-lz 
+ 
++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_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c
+ 
+-# should autodetect system
+-SYS = UNIX
+-ifdef SystemRoot
+-  SYS = WIN
+-else
+-  UNAME := $(shell uname)
+-  ifeq ($(UNAME), Darwin)
+-    SYS = MAC
+-  endif
+-endif
+-
+-CFLAGS=-Wall -O2
+-BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
+-LINKFLAGS=-lm -lpthread -ldl
+-ZLIB=zlib-1.2.8/libz.so.1.2.8
+-
+-ifeq ($(SYS), MAC)
+-  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)
+-  ifeq "$(GCC_GTEQ_43)" "1"
+-    CFLAGS=-Wall -O2 -flax-vector-conversions
+-  endif
+-  BLASFLAGS=-framework Accelerate
+-  LINKFLAGS=-ldl
+-  ZLIB=zlib-1.2.8/libz.1.2.8.dylib
+-endif
+-
+-ifeq ($(SYS), WIN)
+-# Note that, unlike the Linux and Mac build processes, this STATICALLY links
+-# LAPACK, since we have not gotten around to trying dynamically-linked LAPACK
+-# on Windows.
+-# If you don't already have LAPACK built, you'll probably want to turn on
+-# NO_LAPACK.
+-  BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a
+-  LINKFLAGS=-lm -static-libgcc
+-  ZLIB=zlib-1.2.8/libz.a
+-endif
++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_perm.o plink_rserve.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o Rconnection.o hfile.o bgzf.o
+ 
+-ifdef NO_LAPACK
+-  BLASFLAGS=
+-endif
+ 
+-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_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c
++# In the likely event that you are concurrently using PLINK 1.07, we suggest
++# either renaming that binary to "plink1" or this one to "plink2".
+ 
+-# In the event that you are still concurrently using PLINK 1.07, we suggest
+-# renaming that binary to "plink107" and "plink1".  (Previously,
+-# "plink1"/"plink2" was suggested here; that also works for now, but it may
+-# lead to minor problems when PLINK 2.0 is released.)
++# plink: $(SRC)
++# 	g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
+ 
+ plink: $(SRC)
+-	g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
+-
+-plinkw: $(SRC)
+ 	g++ $(CFLAGS) $(SRC) -c
+-	gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
++	gfortran $(OBJ) -o plink2 $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
++	# gfortran $^ -o plink2 -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
+diff --git a/dose2plink.c b/dose2plink.c
+index dc1f33a..ca2d31c 100644
+--- a/dose2plink.c
++++ b/dose2plink.c
+@@ -96,7 +96,7 @@
+   #endif
+ #endif
+ 
+-#include "zlib-1.2.8/zlib.h"
++#include "zlib.h"
+ 
+ #ifdef __APPLE__
+   #include <sys/sysctl.h>
+diff --git a/pigz.c b/pigz.c
+index 46b0525..3ce9a6b 100644
+--- a/pigz.c
++++ b/pigz.c
+@@ -297,7 +297,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <windows.h>
+-#include "zlib-1.2.8/zlib.h"
++#include "zlib.h"
+ 
+ #include "pigz.h"
+ 
+@@ -513,7 +513,7 @@ int32_t flex_pzwrite_close_null(Pigz_state* ps_ptr, char* writep) {
+ #  include <sys/pstat.h>
+ #endif
+ 
+-#include "zlib-1.2.8/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
++#include "zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
+                         /* deflateEnd(), deflateSetDictionary(), crc32(),
+                            inflateBackInit(), inflateBack(), inflateBackEnd(),
+                            Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY,
+diff --git a/plink_common.h b/plink_common.h
+index 84eb929..e0b5cca 100644
+--- a/plink_common.h
++++ b/plink_common.h
+@@ -177,7 +177,7 @@
+ #define VEC_BITS (VEC_BYTES * 8)
+ #define VEC_BITS_M1 (VEC_BITS - 1)
+ 
+-#include "zlib-1.2.8/zlib.h"
++#include "zlib.h"
+ #include "SFMT.h"
+ 
+ // 64MB of non-workspace memory guaranteed for now.