New upstream version 1.90~b6.11-191024 (801326a8) · Commits · Debian Med / plink1.9

Makefile

+5 −3

Original line number	Diff line number	Diff line
		@@ -31,9 +31,6 @@ CC ?= gcc
		CXX ?= g++
		CFLAGS ?= -Wall -O2
		CXXFLAGS ?= -Wall -O2
		BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
		LDFLAGS ?= -lm -lpthread -ldl
		ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11

		PREFIX ?= /usr/local
		DESTDIR ?= .
		@@ -61,6 +58,11 @@ ifeq ($(SYS), WIN)
		ZLIB ?= ../zlib-1.2.11/libz.a
		endif

		# These must appear after the MAC/WIN-specific ?= statements.
		BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
		LDFLAGS ?= -lm -lpthread -ldl
		ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11

		ifdef NO_LAPACK
		BLASFLAGS=
		endif

Makefile.std

+5 −3

Original line number	Diff line number	Diff line
		@@ -31,9 +31,6 @@ CC ?= gcc
		CXX ?= g++
		CFLAGS ?= -Wall -O2
		CXXFLAGS ?= -Wall -O2
		BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
		LDFLAGS ?= -lm -lpthread -ldl
		ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11

		PREFIX ?= /usr/local
		DESTDIR ?= .
		@@ -61,6 +58,11 @@ ifeq ($(SYS), WIN)
		ZLIB ?= ../zlib-1.2.11/libz.a
		endif

		# These must appear after the MAC/WIN-specific ?= statements.
		BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
		LDFLAGS ?= -lm -lpthread -ldl
		ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11

		ifdef NO_LAPACK
		BLASFLAGS=
		endif

plink.c

+12 −3

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

		static const char ver_str[] =
		#ifdef STABLE_BUILD
		"PLINK v1.90b6.10"
		"PLINK v1.90b6.11"
		#else
		"PLINK v1.90p"
		#endif
		@@ -105,7 +105,7 @@ static const char ver_str[] =
		#else
		" 32-bit"
		#endif
		" (17 Jun 2019)";
		" (24 Oct 2019)";
		static const char ver_str2[] =
		// include leading space if day < 10, so character length stays the same
		""
		@@ -7531,7 +7531,7 @@ int32_t main(int32_t argc, char** argv) {
		goto main_ret_INVALID_CMDLINE_2A;
		}
		// may want to permit decimal here
		if (scan_posint_defcapx(argv[cur_arg + 1], &ld_info.prune_window_size) \|\| ((ld_info.prune_window_size == 1) && (param_ct == 3))) {
		if (scan_posint_defcap(argv[cur_arg + 1], &ld_info.prune_window_size) \|\| ((ld_info.prune_window_size == 1) && (param_ct == 3))) {
		sprintf(g_logbuf, "Error: Invalid --%s window size '%s'.\n", argptr, argv[cur_arg + 1]);
		goto main_ret_INVALID_CMDLINE_WWA;
		}
		@@ -8218,6 +8218,10 @@ int32_t main(int32_t argc, char** argv) {
		goto main_ret_NOMEM;
		}
		} else if (!memcmp(argptr2, "d-snps", 7)) {
		if (ld_info.snpstr) {
		logerrprint("Error: --ld-snps cannot be used with --ld-snp or --ld-snp-list.\n");
		goto main_ret_INVALID_CMDLINE_A;
		}
		if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 0x7fffffff)) {
		goto main_ret_INVALID_CMDLINE_2A;
		}
		@@ -8226,6 +8230,10 @@ int32_t main(int32_t argc, char** argv) {
		goto main_ret_1;
		}
		} else if (!memcmp(argptr2, "d-snp-list", 11)) {
		if (ld_info.snpstr) {
		logerrprint("Error: --ld-snp cannot be used with --ld-snp-list.\n");
		goto main_ret_INVALID_CMDLINE_A;
		}
		if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 1)) {
		goto main_ret_INVALID_CMDLINE_2A;
		}
		@@ -10756,6 +10764,7 @@ int32_t main(int32_t argc, char** argv) {
		ld_info.modifier \|= LD_R2;
		} else if (ld_info.window_r2 != 0.2) {
		logerrprint("Error: --ld-window-r2 flag cannot be used with --r.\n");
		goto main_ret_INVALID_CMDLINE_A;
		}
		if (matrix_flag_state) {
		matrix_flag_state = 2;

plink_calc.c

+8 −0

Original line number	Diff line number	Diff line
		@@ -7121,6 +7121,11 @@ int32_t calc_pca(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outna
		}
		fill_int_zero(liwork * (sizeof(__CLPK_integer) / sizeof(int32_t)), (int32_t*)iwork);
		dsyevr_(&jobz, &range, &uplo, &mdim, main_matrix, &mdim, &nz, &nz, &i1, &i2, &zz, &out_m, out_w, out_z, &ldz, isuppz, work, &lwork, iwork, &liwork, &info);
		if ((info != 0) \|\| (out_w[0] != out_w[0])) {
		logprint("\n");
		logerrprint("Error: Failed to extract eigenvector(s) from GRM.\n");
		goto calc_pca_ret_DEGENERATE_DATA;
		}

		// * out_w[0..(pc_ct-1)] contains eigenvalues
		// * out_z[(iiulii)..(iiulii + ulii - 1)] is eigenvector corresponding to
		@@ -7437,6 +7442,9 @@ int32_t calc_pca(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outna
		calc_pca_ret_WRITE_FAIL:
		retval = RET_WRITE_FAIL;
		break;
		calc_pca_ret_DEGENERATE_DATA:
		retval = RET_DEGENERATE_DATA;
		break;
		}
		return retval;
		}

plink_common.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -319,6 +319,7 @@
		#define RET_ALL_SAMPLES_EXCLUDED 11
		#define RET_ALL_MARKERS_EXCLUDED 12
		#define RET_NETWORK 13
		#define RET_DEGENERATE_DATA 14
		#define LOAD_PHENO_LAST_COL 127

		// for 2.0 -> 1.9 backports