Commit 868d9efd authored by Dylan Aïssi's avatar Dylan Aïssi
Browse files

New upstream version 1.90~b6.6-181012

parent 0cb99996

Makefile

+1 −1
Original line number Diff line number Diff line
@@ -31,7 +31,7 @@ CC ?= gcc 
CXX ?=		g++

CFLAGS ?=	-Wall -O2

CXXFLAGS ?=	-Wall -O2

BLASFLAGS ?=	-L/usr/lib64/atlas -llapack -lcblas -latlas

BLASFLAGS ?=	-L/usr/lib64/atlas -llapack -lblas -lcblas -latlas

LDFLAGS ?=	-lm -lpthread -ldl

ZLIB ?=		../zlib-1.2.11/libz.so.1.2.11

Makefile.std

+1 −1
Original line number Diff line number Diff line
@@ -31,7 +31,7 @@ CC ?= gcc 
CXX ?=		g++

CFLAGS ?=	-Wall -O2

CXXFLAGS ?=	-Wall -O2

BLASFLAGS ?=	-L/usr/lib64/atlas -llapack -lcblas -latlas

BLASFLAGS ?=	-L/usr/lib64/atlas -llapack -lblas -lcblas -latlas

LDFLAGS ?=	-lm -lpthread -ldl

ZLIB ?=		../zlib-1.2.11/libz.so.1.2.11

plink.c

+2 −2
Original line number Diff line number Diff line
@@ -93,7 +93,7 @@ 








static const char ver_str[] =









#ifdef STABLE_BUILD









  "PLINK v1.90b6.5"









  "PLINK v1.90b6.6"









#else









  "PLINK v1.90p"









#endif








@@ -105,7 +105,7 @@ static const char ver_str[] =







#else









  " 32-bit"









#endif









  " (13 Sep 2018)";









  " (12 Oct 2018)";









static const char ver_str2[] =









  // include leading space if day < 10, so character length stays the same









  ""
































plink_common.h



+44
−11






























Original line number
Diff line number
Diff line







@@ -27,6 +27,9 @@







#include <string.h>









#include <math.h>









#include <stdint.h>









#ifndef __STDC_FORMAT_MACROS









#  define __STDC_FORMAT_MACROS 1









#endif









#include <inttypes.h>



















// avoid compiler warning








@@ -59,7 +62,13 @@







  // needed for MEMORYSTATUSEX









  #ifndef _WIN64









    #define WINVER 0x0500









  #else









    #define __LP64__









  #endif









  #ifndef WIN32_LEAN_AND_MEAN









    #define WIN32_LEAN_AND_MEAN









  #endif









  #include <windows.h>









#else // Unix









  #include <sys/stat.h>









#endif








@@ -77,12 +86,13 @@







#endif



















#ifdef _WIN32









  #define PRId64 "I64d"









  #define PRIu64 "I64u"









  #define fseeko fseeko64









  #define ftello ftello64









  #include <windows.h>









  #include <process.h>









#  undef PRId64









#  undef PRIu64









#  define PRId64 "I64d"









#  define PRIu64 "I64u"









  #define pthread_t HANDLE









  #define THREAD_RET_TYPE unsigned __stdcall









  #define THREAD_RETURN return 0








@@ -96,8 +106,10 @@







    #define getc_unlocked getc









    #define putc_unlocked putc









  #endif









  #if __cplusplus < 201103L









    #define uint64_t unsigned long long









    #define int64_t long long









  #endif









#else









  #include <pthread.h>









  #define THREAD_RET_TYPE void*








@@ -144,6 +156,27 @@

















#ifdef __cplusplus









  #include <algorithm>









#  ifdef _WIN32









// Windows C++11 <algorithm> resets these values :(









#    undef PRIu64









#    undef PRId64









#    define PRIu64 "I64u"









#    define PRId64 "I64d"









#    undef PRIuPTR









#    undef PRIdPTR









#    ifdef __LP64__









#      define PRIuPTR PRIu64









#      define PRIdPTR PRId64









#    else









#      if __cplusplus < 201103L









#        define PRIuPTR "lu"









#        define PRIdPTR "ld"









#      else









#        define PRIuPTR "u"









#        define PRIdPTR "d"









#      endif









#    endif









#  endif









  #define HEADER_INLINE inline









#else









  #define HEADER_INLINE static inline








@@ -206,10 +239,10 @@

















  #define ZEROLU 0LU









  #define ONELU 1LU









  #ifndef PRIuPTR









#  if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8) && (__cplusplus < 201103L)









#    undef PRIuPTR









#    undef PRIdPTR









#    define PRIuPTR "lu"









  #endif









  #ifndef PRIdPTR









#    define PRIdPTR "ld"









#  endif









  #define PRIxPTR2 "08lx"
































plink_family.c



+3
−2






























Original line number
Diff line number
Diff line







@@ -1749,6 +1749,7 @@ int32_t tdt_poo(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* o







  // entry bit 16 & 24: hhh?









  // entry bit 17: paternal A1 transmitted?









  // entry bit 25: maternal A1 transmitted?









  // bugfix (10 Oct 2018): missed a few chrX possibilities









  const uint32_t poo_table[] =









    {0, 0, 0, 0,









     0, 0, 0, 0,








@@ -1758,10 +1759,10 @@ int32_t tdt_poo(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* o







     0, 0, 0, 0,









     0, 0, 0, 0,









     0, 0, 0, 0,









     0x2000200, 0, 0x200, 0,









     0x2000200, 0, 0x200, 0x200,









     0, 0, 0, 0,









     0x2020202, 0, 0x1010202, 0x202,









     0, 0, 0x2000200, 0x200,









     0x2000200, 0, 0x2000200, 0x200,









     0, 0, 0, 0,









     0, 0, 0, 0,









     0, 0, 0x20002, 2};