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Makefile
View file @ cda5f058
......@@ -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
View file @ cda5f058
......@@ -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
......
debian/changelog
View file @ cda5f058
plink1.9 (1.90~b6.6-181012-1) UNRELEASED; urgency=medium
* New upstream release.
* Update my email address.
-- Dylan Aïssi <daissi@debian.org> Thu, 01 Nov 2018 07:30:31 +0100
plink1.9 (1.90~b6.5-180913-1) unstable; urgency=medium
* New upstream release.
......
debian/control
View file @ cda5f058
Source: plink1.9
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Dylan Aïssi <bob.dybian@gmail.com>
Uploaders: Dylan Aïssi <daissi@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
......
debian/upstream.docs/upstream.changelog
View file @ cda5f058
# Copy/Paste from https://www.cog-genomics.org/plink/1.9/
13 Sep 2018: Improved logistic regression convergence-failure detection (affects case/control --epistasis as well as --logistic). Fixed --R memory leak.
10 Oct 2018: Fixed --tdt parent-of-origin-analysis handling of chrX.
13 Sep: Improved logistic regression convergence-failure detection (affects case/control --epistasis as well as --logistic). Fixed --R memory leak.
7 Aug: --assoc set-test bugfix.
......
plink.c
View file @ cda5f058
......@@ -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
View file @ cda5f058
......@@ -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
View file @ cda5f058
......@@ -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};
......
plink_matrix.c
View file @ cda5f058
......@@ -286,7 +286,7 @@ int32_t invert_matrix(int32_t dim, double* matrix, MATRIX_INVERT_BUF1_TYPE* dbl_
}
return 0;
}
#else
#else // !NOLAPACK
int32_t invert_matrix(__CLPK_integer dim, double* matrix, MATRIX_INVERT_BUF1_TYPE* int_1d_buf, double* dbl_2d_buf) {
// dgetrf_/dgetri_ is more efficient than dpotrf_/dpotri_ on OS X.
__CLPK_integer lwork = dim * dim;
......@@ -321,7 +321,7 @@ int32_t invert_matrix_checked(__CLPK_integer dim, double* matrix, MATRIX_INVERT_
dgetri_(&dim, matrix, &dim, int_1d_buf, dbl_2d_buf, &lwork, &info);
return 0;
}
#endif
#endif // !NOLAPACK
void col_major_matrix_multiply(__CLPK_integer row1_ct, __CLPK_integer col2_ct, __CLPK_integer common_ct, double* inmatrix1, double* inmatrix2, double* outmatrix) {
#ifdef NOLAPACK
......@@ -345,15 +345,15 @@ void col_major_matrix_multiply(__CLPK_integer row1_ct, __CLPK_integer col2_ct, _
}
}
#else
#ifdef _WIN32
# ifndef USE_CBLAS_XGEMM
char blas_char = 'N';
double dyy = 1;
double dzz = 0;
dgemm_(&blas_char, &blas_char, &row1_ct, &col2_ct, &common_ct, &dyy, inmatrix1, &row1_ct, inmatrix2, &common_ct, &dzz, outmatrix, &row1_ct);
# else
cblas_dgemm(CblasColMajor, CblasNoTrans, CblasNoTrans, row1_ct, col2_ct, common_ct, 1.0, inmatrix1, row1_ct, inmatrix2, common_ct, 0.0, outmatrix, row1_ct);
#endif // _WIN32
#endif // NOLAPACK
# endif // USE_CBLAS_XGEMM
#endif // !NOLAPACK
}
void col_major_fmatrix_multiply(__CLPK_integer row1_ct, __CLPK_integer col2_ct, __CLPK_integer common_ct, float* inmatrix1, float* inmatrix2, float* outmatrix) {
......@@ -378,15 +378,15 @@ void col_major_fmatrix_multiply(__CLPK_integer row1_ct, __CLPK_integer col2_ct,
}
}
#else
#ifdef _WIN32
# ifndef USE_CBLAS_XGEMM
char blas_char = 'N';
float fyy = 1;
float fzz = 0;
sgemm_(&blas_char, &blas_char, &row1_ct, &col2_ct, &common_ct, &fyy, inmatrix1, &row1_ct, inmatrix2, &common_ct, &fzz, outmatrix, &row1_ct);
# else
cblas_sgemm(CblasColMajor, CblasNoTrans, CblasNoTrans, row1_ct, col2_ct, common_ct, 1.0, inmatrix1, row1_ct, inmatrix2, common_ct, 0.0, outmatrix, row1_ct);
#endif // _WIN32
#endif // NOLAPACK
# endif // USE_CBLAS_XGEMM
#endif // !NOLAPACK
}
// Todo: replace these with cache-oblivious, or at least -friendlier,
......
plink_matrix.h
View file @ cda5f058
......@@ -19,17 +19,7 @@
// Wrappers for frequent LAPACK calls (sometimes with no-LAPACK fallbacks).
// May want to make this comprehensive to make linking with Intel MKL practical
// in the future.
// todo: allow this to take advantage of 64-bit integer LAPACK. As of this
// writing, it's available on Amazon EC2 64-bit Linux instances, but I can't
// find it for Windows. (And even if OS X vecLib adds it soon, we can't use it
// there anytime soon because static linking is not an option.)
#ifdef __APPLE__
#include <Accelerate/Accelerate.h>
#endif
// (Update, 11 Oct 2018: Backported PLINK 2.0's MKL support.)
#ifdef NOLAPACK
......@@ -38,47 +28,109 @@
# define MATRIX_INVERT_BUF1_CHECKED_ALLOC (2 * sizeof(double))
# define __CLPK_integer int
#else // not NOLAPACK
#else // !NOLAPACK
# ifdef __APPLE__
# include <Accelerate/Accelerate.h>
# define USE_CBLAS_XGEMM
# endif
# ifndef __APPLE__
# ifdef __cplusplus
extern "C" {
# endif
typedef double __CLPK_doublereal;
# if defined(__LP64__) || defined(_WIN32)
typedef int32_t __CLPK_integer;
# else
typedef long int __CLPK_integer;
# endif
# ifdef _WIN32
// openblas is easy enough to set up on Windows nowadays.
// not worth the trouble of ripping out vector extensions, etc. just so we
// can compile with Visual Studio and gain access to MKL.
// (todo: upgrade from 0.2.19 to a later version, build setup will probably
// need to change a bit)
# define HAVE_LAPACK_CONFIG_H
# define LAPACK_COMPLEX_STRUCTURE
#include "lapack/lapacke/include/lapacke.h"
typedef int32_t __CLPK_integer;
# include "lapacke.h"
__CLPK_doublereal ddot_(__CLPK_integer* n, __CLPK_doublereal* dx,
__CLPK_integer* incx, __CLPK_doublereal* dy,
__CLPK_integer* incy);
void dger_(int* m, int* n, double* alpha, double* x, int* incx, double* y,
int* incy, double* a, int* lda);
void dgemm_(char* transa, char* transb, int* m, int* n, int* k,
double* alpha, double* a, int* lda, double* b, int* ldb,
double* beta, double* c, int* ldc);
void dgemm_(char* transa, char* transb, __CLPK_integer* m, __CLPK_integer* n,
__CLPK_integer* k, double* alpha, double* a, __CLPK_integer* lda,
double* b, __CLPK_integer* ldb, double* beta, double* c,
__CLPK_integer* ldc);
void dsymv_(char* uplo, int* n, double* alpha, double* a, int* lda,
double* x, int* incx, double* beta, double* y, int* incy);
double ddot_(int* n, double* dx, int* incx, double* dy, int* incy);
void dgetrf_(__CLPK_integer* m, __CLPK_integer* n,
__CLPK_doublereal* a, __CLPK_integer* lda,
__CLPK_integer* ipiv, __CLPK_integer* info);
void sgemm_(char* transa, char* transb, int* m, int* n, int* k,
float* alpha, float* a, int* lda, float* b, int* ldb,
float* beta, float* c, int* ldc);
void sgemm_(char* transa, char* transb, __CLPK_integer* m, __CLPK_integer* n,
__CLPK_integer* k, float* alpha, float* a, __CLPK_integer* lda,
float* b, __CLPK_integer* ldb, float* beta, float* c,
__CLPK_integer* ldc);
#else // not _WIN32
# else // Linux
# ifdef USE_MKL
# ifndef __LP64__
# error "32-bit Linux build does not support Intel MKL."
# endif
# define USE_CBLAS_XGEMM
// sizeof(MKL_INT) should be 4.
# define MKL_LP64
# ifdef DYNAMIC_MKL
# include <mkl_service.h>
# include <mkl_cblas.h>
# include <mkl_lapack.h>
# else
# include "mkl_service.h"
# include "mkl_cblas.h"
# include "mkl_lapack.h"
# endif
# else
# ifdef USE_CBLAS_XGEMM
# include <cblas.h>
#ifdef __LP64__
typedef int32_t __CLPK_integer;
# else
typedef long int __CLPK_integer;
// ARGH
// cmake on Ubuntu 14 seems to require use of cblas_f77.h instead of cblas.h.
// Conversely, cblas_f77.h does not seem to be available on the Scientific
// Linux ATLAS/LAPACK install, and right now that's my only option for
// producing 32-bit static builds...
// So. Default include is cblas.h. To play well with cmake + Ubuntu 14 and
// 16 simultaneously, there is a CBLAS_F77_ON_OLD_GCC mode which picks
// cblas_f77.h on Ubuntu 14 and cblas.h on 16.
# ifdef FORCE_CBLAS_F77
# include <cblas_f77.h>
# elif !defined(CBLAS_F77_ON_OLD_GCC)
# include <cblas.h>
# else
# if (__GNUC__ <= 4)
# include <cblas_f77.h>
# else
# if __has_include(<cblas.h>)
# include <cblas.h>
# else
# include <cblas_f77.h>
# endif
# endif
# endif
__CLPK_doublereal ddot_(__CLPK_integer* n, __CLPK_doublereal* dx,
__CLPK_integer* incx, __CLPK_doublereal* dy,
__CLPK_integer* incy);
# endif
int dgetrf_(__CLPK_integer* m, __CLPK_integer* n,
__CLPK_doublereal* a, __CLPK_integer* lda,
__CLPK_integer* ipiv, __CLPK_integer* info);
......@@ -118,20 +170,39 @@ extern "C" {
__CLPK_doublereal* vt, __CLPK_integer* ldvt,
__CLPK_doublereal* work, __CLPK_integer* lwork,
__CLPK_integer* iwork, __CLPK_integer* info);
# ifndef USE_CBLAS_XGEMM
void dgemm_(char* transa, char* transb, __CLPK_integer* m, __CLPK_integer* n,
__CLPK_integer* k, double* alpha, double* a, __CLPK_integer* lda,
double* b, __CLPK_integer* ldb, double* beta, double* c,
__CLPK_integer* ldc);
void dsymv_(char* uplo, int* n, double* alpha, double* a, int* lda,
double* x, int* incx, double* beta, double* y, int* incy);
void sgemm_(char* transa, char* transb, __CLPK_integer* m, __CLPK_integer* n,
__CLPK_integer* k, float* alpha, float* a, __CLPK_integer* lda,
float* b, __CLPK_integer* ldb, float* beta, float* c,
__CLPK_integer* ldc);
# endif
# endif // !USE_MKL
# endif
void xerbla_(void);
# ifdef __cplusplus
}
#endif // __cplusplus
#endif // __APPLE__
} // extern "C"
# endif
# endif // !__APPLE__
# define MATRIX_INVERT_BUF1_TYPE __CLPK_integer
# define MATRIX_INVERT_BUF1_ELEM_ALLOC sizeof(__CLPK_integer)
// invert_matrix_checked() usually requires a larger buffer
# define MATRIX_INVERT_BUF1_CHECKED_ALLOC (2 * sizeof(__CLPK_integer))
#endif // NOLAPACK
#endif // !NOLAPACK
#define MATRIX_SINGULAR_RCOND 1e-14
......
plink_rserve.c
View file @ cda5f058
......@@ -20,14 +20,14 @@
// gcc instead of g++.
#if defined __cplusplus && !defined _WIN32
#include "plink_common.h"
#include "plink_cluster.h"
#define MAIN
#define SOCK_ERRORS
#include "sisocks.h"
#include "Rconnection.h"
#include "plink_common.h"
#include "plink_cluster.h"
#define RPLUGIN_BLOCK_SIZE 100
int32_t rserve_call(char* rplugin_fname, char* rplugin_host_or_socket, int32_t rplugin_port, uint32_t rplugin_debug, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, char** marker_allele_ptrs, uint32_t* marker_pos, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* pheno_nm, uint32_t pheno_nm_ct, uintptr_t* pheno_c, double* pheno_d, uint32_t cluster_ct, uint32_t* cluster_map, uint32_t* cluster_starts, uintptr_t covar_ct, double* covar_d, char* outname, char* outname_end) {
......
toy.ped
View file @ cda5f058
1 1000000000 0 0 1 1 0 0 1 1
1 1000000001 0 0 1 2 1 1 1 2
1 1000000000 0 0 1 1 0 0 A A
1 1000000001 0 0 1 2 C C A G