New upstream version 1.90~b5.4-180410 (c271b712) · Commits · Debian Med / plink1.9

plink.c

+4 −3

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

		static const char ver_str[] =
		#ifdef STABLE_BUILD
		"PLINK v1.90b5.3"
		"PLINK v1.90b5.4"
		#else
		"PLINK v1.90p"
		#endif
		@@ -105,7 +105,7 @@ static const char ver_str[] =
		#else
		" 32-bit"
		#endif
		" (21 Feb 2018)";
		" (10 Apr 2018)";
		static const char ver_str2[] =
		// include leading space if day < 10, so character length stays the same
		""
		@@ -12801,7 +12801,8 @@ int32_t main(int32_t argc, char** argv) {
		if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 1)) {
		goto main_ret_INVALID_CMDLINE_2A;
		}
		retval = alloc_fname(&cluster.zerofname, argv[cur_arg + uii], argptr, 0);
		// bugfix (9 Apr 2018): had wrong array index
		retval = alloc_fname(&cluster.zerofname, argv[cur_arg + 1], argptr, 0);
		if (retval) {
		goto main_ret_1;
		}

+3 −1

Original line number	Diff line number	Diff line
		@@ -532,7 +532,9 @@ int32_t multcomp(char* outname, char* outname_end, uint32_t* marker_uidxs, uintp
		adjust_print_log10(pv_gc[cur_idx], output_min_p, output_min_p_str, output_min_p_strlen, &bufptr);
		}
		if (qq_plot) {
		bufptr = dtoa_g_wxp4x((((double)((int32_t)cur_idx)) + 0.5) * dzz, 10, ' ', bufptr);
		// quasi-bugfix (23 Mar 2018): this should be logscale, both for
		// consistency with plink 1.07 and because it makes more sense
		bufptr = dtoa_g_wxp4x(-log10((((double)((int32_t)cur_idx)) + 0.5) * dzz), 10, ' ', bufptr);
		}
		adjust_print_log10(bonf, output_min_p, output_min_p_str, output_min_p_strlen, &bufptr);
		adjust_print_log10(pv_holm, output_min_p, output_min_p_str, output_min_p_strlen, &bufptr);

+3 −3

Original line number	Diff line number	Diff line
		@@ -4621,11 +4621,11 @@ int32_t oxford_to_bed(char* genname, char* samplename, char* outname, char* outn
		const uint32_t layout = (uii >> 2) & 15;
		const uint32_t compression_mode = uii & 3;
		if ((layout == 2) && (compression_mode != 3)) {
		LOGERRPRINTF("Error: BGEN v1.%c input requires PLINK 2.0 (under development as of this\nwriting). Use gen-convert to downcode to BGEN v1.1 if you want to process this\ndata with PLINK 1.9.\n", (compression_mode == 2)? '3' : '2');
		LOGERRPRINTF("Error: BGEN v1.%c input requires PLINK 2.0 (under development as of this\nwriting). Use qctool2 or bgenix to downcode to BGEN v1.1 if you want to\nprocess this data with PLINK 1.9.\n", (compression_mode == 2)? '3' : '2');
		} else if (layout > 2) {
		logerrprint("Error: Unrecognized BGEN version. Use gen-convert or a similar tool to\ndowncode to BGEN v1.1 if you want to process this data with PLINK 1.9.\n");
		logerrprint("Error: Unrecognized BGEN version. Use bgenix or a similar tool to downcode to\nBGEN v1.1 if you want to process this data with PLINK 1.9.\n");
		} else {
		logerrprint("Error: Unrecognized flags in .bgen header. (PLINK 1.9 only supports\nBGEN v1.0 and v1.1.)\n");
		logerrprint("Error: Unrecognized flags in .bgen header. (PLINK 1.9 only supports BGEN v1.0\nand v1.1.)\n");
		}
		goto oxford_to_bed_ret_INVALID_FORMAT;
		}

+7 −5

Original line number	Diff line number	Diff line
		@@ -509,12 +509,14 @@ uint32_t erase_mendel_errors(uintptr_t unfiltered_sample_ct, uintptr_t* loadbuf,
		unn = uii / BITCT2;
		uoo = ujj / BITCT2;
		upp = ukk / BITCT2;
		uii = 2 * (uii % BITCT2);
		const uint32_t uqq = 2 * (uii % BITCT2);
		ujj = 2 * (ujj % BITCT2);
		ukk = 2 * (ukk % BITCT2);
		ulii = (workbuf[unn] >> uii) & 3;
		ulii = (workbuf[unn] >> uqq) & 3;
		uljj = ((workbuf[uoo] >> ujj) & 3) \| (((workbuf[upp] >> ukk) & 3) << 2);
		if (ulii != 1) {
		// bugfix (10 Apr 2018): is_set(sex_male, uii) didn't work since we had
		// replaced the value with twice the low-order bits
		if ((!is_x) \|\| (!is_set(sex_male, uii))) {
		umm = mendel_error_table[ulii \| (uljj << 2)];
		} else {
		@@ -522,7 +524,7 @@ uint32_t erase_mendel_errors(uintptr_t unfiltered_sample_ct, uintptr_t* loadbuf,
		}
		if (umm) {
		ulii = loadbuf[unn];
		uljj = ONELU << uii;
		uljj = ONELU << uqq;
		loadbuf[unn] = (ulii & (~(3 * uljj))) \| uljj;
		if (umm & 0x100) {
		ulii = loadbuf[uoo];
		@@ -539,9 +541,9 @@ uint32_t erase_mendel_errors(uintptr_t unfiltered_sample_ct, uintptr_t* loadbuf,
		} else if (!uljj) {
		// both parents are homozygous for the same allele, so child genotype
		// is "known" for the purpose of checking grandchild genotypes
		workbuf[unn] &= ~(ONELU << uii);
		workbuf[unn] &= ~(ONELU << uqq);
		} else if (uljj == 15) {
		workbuf[unn] \|= (2 * ONELU) << uii;
		workbuf[unn] \|= (2 * ONELU) << uqq;
		}
		// no need to fill "known" heterozygous genotype, since that's treated
		// the same way as a missing genotype

+2 −1

Original line number	Diff line number	Diff line
		@@ -1485,7 +1485,8 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		" --missing-phenotype [v] : Set missing phenotype value (normally -9).\n"
		" --1 : Expect case/control phenotypes to be coded as\n"
		" 0 = control, 1 = case, instead of the usual\n"
		" 0 = missing, 1 = control, 2 = case.\n"
		" 0 = missing, 1 = control, 2 = case. This also\n"
		" forces phenotypes to be interpreted as case/ctrl.\n"
		);
		help_print("make-pheno\tpheno", &help_ctrl, 0,
		" --make-pheno [fn] [val] : Define a new case/control phenotype. If the val\n"

+6 −6

File changed.

Contains only whitespace changes.