New upstream version 1.90~b6.12-191028 (f1257bee) · Commits · Debian Med / plink1.9

plink.c

+17 −3

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

		static const char ver_str[] =
		#ifdef STABLE_BUILD
		"PLINK v1.90b6.11"
		"PLINK v1.90b6.12"
		#else
		"PLINK v1.90p"
		#endif
		@@ -105,7 +105,7 @@ static const char ver_str[] =
		#else
		" 32-bit"
		#endif
		" (24 Oct 2019)";
		" (28 Oct 2019)";
		static const char ver_str2[] =
		// include leading space if day < 10, so character length stays the same
		""
		@@ -3167,6 +3167,7 @@ int32_t main(int32_t argc, char** argv) {
		char* metaanal_a1field_search_order = nullptr;
		char* metaanal_a2field_search_order = nullptr;
		char* metaanal_pfield_search_order = nullptr;
		char* metaanal_sefield_search_order = nullptr;
		char* metaanal_essfield_search_order = nullptr;
		char* rplugin_fname = nullptr;
		char* rplugin_host_or_socket = nullptr;
		@@ -9480,6 +9481,18 @@ int32_t main(int32_t argc, char** argv) {
		if (retval) {
		goto main_ret_NOMEM;
		}
		} else if (!memcmp(argptr2, "eta-analysis-se-field", 22)) {
		if (!metaanal_fnames) {
		logerrprint("Error: --meta-analysis-se-field must be used with --meta-analysis.\n");
		goto main_ret_INVALID_CMDLINE;
		}
		if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 0x10000000)) {
		goto main_ret_INVALID_CMDLINE_2A;
		}
		retval = alloc_and_flatten(&metaanal_sefield_search_order, &(argv[cur_arg + 1]), param_ct);
		if (retval) {
		goto main_ret_NOMEM;
		}
		} else if (!memcmp(argptr2, "eta-analysis-ess-field", 23)) {
		if ((!metaanal_fnames) \|\| (!(metaanal_flags & METAANAL_WEIGHTED_Z))) {
		logerrprint("Error: --meta-analysis-ess-field must be used with --meta-analysis + weighted-z.\n");
		@@ -13369,7 +13382,7 @@ int32_t main(int32_t argc, char** argv) {
		if (metaanal_fnames) {
		// possible todo: make this support --aec (takes a bit of work since
		// chromosome byte in data structure must be widened)
		retval = meta_analysis(metaanal_fnames, metaanal_snpfield_search_order, metaanal_a1field_search_order, metaanal_a2field_search_order, metaanal_pfield_search_order, metaanal_essfield_search_order, metaanal_flags, (misc_flags & MISC_EXTRACT_RANGE)? nullptr : extractname, outname, outname_end, output_min_p, &chrom_info);
		retval = meta_analysis(metaanal_fnames, metaanal_snpfield_search_order, metaanal_a1field_search_order, metaanal_a2field_search_order, metaanal_pfield_search_order, metaanal_sefield_search_order, metaanal_essfield_search_order, metaanal_flags, (misc_flags & MISC_EXTRACT_RANGE)? nullptr : extractname, outname, outname_end, output_min_p, &chrom_info);
		if (retval) {
		goto main_ret_1;
		}
		@@ -13634,6 +13647,7 @@ int32_t main(int32_t argc, char** argv) {
		free_cond(metaanal_a1field_search_order);
		free_cond(metaanal_a2field_search_order);
		free_cond(metaanal_pfield_search_order);
		free_cond(metaanal_sefield_search_order);
		free_cond(metaanal_essfield_search_order);
		free_cond(rplugin_fname);
		free_cond(rplugin_host_or_socket);

plink_help.c

+8 −7

Original line number	Diff line number	Diff line
		@@ -2064,14 +2064,15 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		help_print("clump-best\tclump", &help_ctrl, 0,
		" --clump-best : Report best proxy for each --clump index var.\n"
		);
		help_print("meta-analysis-snp-field\tmeta-analysis-a1-field\tmeta-analysis-a2-field\tmeta-analysis-p-field\tmeta-analysis-ess-field\tmeta-analysis", &help_ctrl, 0,
		help_print("meta-analysis-snp-field\tmeta-analysis-a1-field\tmeta-analysis-a2-field\tmeta-analysis-p-field\tmeta-analysis-se-field\tmeta-analysis-ess-field\tmeta-analysis", &help_ctrl, 0,
		" --meta-analysis-snp-field <n...> : Set --meta-analysis variant ID, A1/A2\n"
		" --meta-analysis-a1-field <n...> allele, p-value, and/or effective sample\n"
		" --meta-analysis-a2-field <n...> size field names. Defauls are 'SNP',\n"
		" --meta-analysis-p-field <n...> 'A1', 'A2', 'P', and 'NMISS',\n"
		" --meta-analysis-ess-field <n...> respectively. When multiple parameters\n"
		" are given to these flags, earlier names\n"
		" take precedence over later ones.\n"
		" --meta-analysis-a1-field <n...> allele, p-value, standard error, and/or\n"
		" --meta-analysis-a2-field <n...> effective sample size field names.\n"
		" --meta-analysis-p-field <n...> Defaults are 'SNP', 'A1', 'A2', 'P', 'SE',\n"
		" --meta-analysis-se-field <n...> and 'NMISS', respectively. When multiple\n"
		" --meta-analysis-ess-field <n...> parameters are given to these flags,\n"
		" earlier names take precedence over later\n"
		" ones.\n"
		" Note that, if the numbers of cases and\n"
		" controls are unequal, effective sample\n"
		" size should be\n"

plink_misc.c

+41 −15

Original line number	Diff line number	Diff line
		@@ -4930,6 +4930,7 @@ int32_t meta_analysis_open_and_read_header(const char* fname, char* loadbuf, uin
		uint32_t token_ct = *token_ct_ptr;
		uint32_t best_var_id = 0x7fffffff;
		uint32_t best_p_id = 0x7fffffff;
		uint32_t best_se_id = 0x7fffffff;
		uint32_t best_ess_id = 0x7fffffff;
		uint32_t best_a1_id = 0x7fffffff;
		uint32_t best_a2_id = 0x7fffffff;
		@@ -4999,6 +5000,15 @@ int32_t meta_analysis_open_and_read_header(const char* fname, char* loadbuf, uin
		}
		break;
		case 2:
		// SE
		if (uii < best_se_id) {
		best_p_id = uii;
		parse_table[2] = (colnum * 16) \| 2;
		} else if (uii == best_se_id) {
		goto meta_analysis_open_and_read_header_ret_DUPLICATE_HEADER_COL;
		}
		break;
		case 3:
		// P
		if (uii < best_p_id) {
		best_p_id = uii;
		@@ -5007,7 +5017,7 @@ int32_t meta_analysis_open_and_read_header(const char* fname, char* loadbuf, uin
		goto meta_analysis_open_and_read_header_ret_DUPLICATE_HEADER_COL;
		}
		break;
		case 3:
		case 4:
		// effective sample size
		if (uii < best_ess_id) {
		best_ess_id = uii;
		@@ -5016,7 +5026,7 @@ int32_t meta_analysis_open_and_read_header(const char* fname, char* loadbuf, uin
		goto meta_analysis_open_and_read_header_ret_DUPLICATE_HEADER_COL;
		}
		break;
		case 4:
		case 5:
		// A1
		if (uii < best_a1_id) {
		best_a1_id = uii;
		@@ -5025,7 +5035,7 @@ int32_t meta_analysis_open_and_read_header(const char* fname, char* loadbuf, uin
		goto meta_analysis_open_and_read_header_ret_DUPLICATE_HEADER_COL;
		}
		break;
		case 5:
		case 6:
		// A2
		if (uii < best_a2_id) {
		best_a2_id = uii;
		@@ -5152,7 +5162,7 @@ static inline uint32_t uint32_decode_5_hi_uchar(const char* start) {
		return uii;
		}

		int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1field_search_order, char* a2field_search_order, char* pfield_search_order, char* essfield_search_order, uint32_t flags, char* extractname, char* outname, char* outname_end, double output_min_p, Chrom_info* chrom_info_ptr) {
		int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1field_search_order, char* a2field_search_order, char* pfield_search_order, char* sefield_search_order, char* essfield_search_order, uint32_t flags, char* extractname, char* outname, char* outname_end, double output_min_p, Chrom_info* chrom_info_ptr) {
		unsigned char* bigstack_mark = g_bigstack_base;
		unsigned char* bigstack_end_mark = g_bigstack_end;
		gzFile gz_infile = nullptr;
		@@ -5162,7 +5172,7 @@ int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1f
		char* sorted_extract_ids = nullptr;
		uintptr_t* duplicate_id_bitfield = nullptr;
		Ll_str** duplicate_id_htable = nullptr;
		uintptr_t header_dict_ct = 2; // 'SE', BETA/OR
		uintptr_t header_dict_ct = 1; // BETA/OR
		uintptr_t max_header_len = 3;
		uintptr_t extract_ct = 0;
		uintptr_t max_extract_id_len = 0;
		@@ -5289,6 +5299,11 @@ int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1f
		max_header_len = 4; // 'SNP' + null terminator
		header_dict_ct++;
		}
		if (sefield_search_order) {
		header_dict_ct += count_and_measure_multistr(sefield_search_order, &max_header_len);
		} else {
		header_dict_ct++;
		}
		if (input_beta && (max_header_len < 5)) {
		max_header_len = 5;
		}
		@@ -5354,12 +5369,23 @@ int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1f
		memcpy(&(sorted_header_dict[ulii * max_header_len]), "BETA", 5);
		}
		header_id_map[ulii++] = 1;
		if (sefield_search_order) {
		bufptr = sefield_search_order;
		uii = 0x20000000;
		do {
		slen = strlen(bufptr) + 1;
		memcpy(&(sorted_header_dict[ulii * max_header_len]), bufptr, slen);
		header_id_map[ulii++] = uii++;
		bufptr = &(bufptr[slen]);
		} while (*bufptr);
		} else {
		memcpyl3(&(sorted_header_dict[ulii * max_header_len]), "SE");
		header_id_map[ulii++] = 2;
		header_id_map[ulii++] = 0x20000000;
		}
		if (weighted_z) {
		if (pfield_search_order) {
		bufptr = pfield_search_order;
		uii = 0x20000000;
		uii = 0x30000000;
		do {
		slen = strlen(bufptr) + 1;
		memcpy(&(sorted_header_dict[ulii * max_header_len]), bufptr, slen);
		@@ -5368,12 +5394,12 @@ int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1f
		} while (*bufptr);
		} else {
		memcpy(&(sorted_header_dict[ulii * max_header_len]), "P", 2);
		header_id_map[ulii++] = 0x20000000;
		header_id_map[ulii++] = 0x30000000;
		}
		if (essfield_search_order) {
		// bugfix (3 Nov 2017): had pfield_search_order here
		bufptr = essfield_search_order;
		uii = 0x30000000;
		uii = 0x40000000;
		do {
		slen = strlen(bufptr) + 1;
		memcpy(&(sorted_header_dict[ulii * max_header_len]), bufptr, slen);
		@@ -5382,7 +5408,7 @@ int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1f
		} while (*bufptr);
		} else {
		memcpy(&(sorted_header_dict[ulii * max_header_len]), "NMISS", 6);
		header_id_map[ulii++] = 0x30000000;
		header_id_map[ulii++] = 0x40000000;
		}
		}
		if (use_map) {
		@@ -5393,7 +5419,7 @@ int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1f
		if (!no_allele) {
		if (a1field_search_order) {
		bufptr = a1field_search_order;
		uii = 0x40000000;
		uii = 0x50000000;
		do {
		slen = strlen(bufptr) + 1;
		memcpy(&(sorted_header_dict[ulii * max_header_len]), bufptr, slen);
		@@ -5402,11 +5428,11 @@ int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1f
		} while (*bufptr);
		} else {
		memcpyl3(&(sorted_header_dict[ulii * max_header_len]), "A1");
		header_id_map[ulii++] = 0x40000000;
		header_id_map[ulii++] = 0x50000000;
		}
		if (a2field_search_order) {
		bufptr = a2field_search_order;
		uii = 0x50000000;
		uii = 0x60000000;
		do {
		slen = strlen(bufptr) + 1;
		memcpy(&(sorted_header_dict[ulii * max_header_len]), bufptr, slen);
		@@ -5415,7 +5441,7 @@ int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1f
		} while (*bufptr);
		} else {
		memcpyl3(&(sorted_header_dict[ulii * max_header_len]), "A2");
		header_id_map[ulii] = 0x50000000;
		header_id_map[ulii] = 0x60000000;
		}
		}
		}

plink_misc.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -105,6 +105,6 @@ int32_t fst_report(FILE* bedfile, uintptr_t bed_offset, char* outname, char* out

		int32_t score_report(Score_info* sc_ip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude_orig, uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, char** marker_allele_ptrs, double* set_allele_freqs, uintptr_t sample_ct, uintptr_t unfiltered_sample_ct, uintptr_t* sample_exclude, char* sample_ids, uint32_t plink_maxfid, uint32_t plink_maxiid, uintptr_t max_sample_id_len, uintptr_t* sex_male, uintptr_t* pheno_nm, uintptr_t* pheno_c, double* pheno_d, char* output_missing_pheno, uint32_t hh_exists, Chrom_info* chrom_info_ptr, char* outname, char* outname_end);

		int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1field_search_order, char* a2field_search_order, char* pfield_search_order, char* essfield_search_order, uint32_t flags, char* extractname, char* outname, char* outname_end, double output_min_p, Chrom_info* chrom_info_ptr);
		int32_t meta_analysis(char* input_fnames, char* snpfield_search_order, char* a1field_search_order, char* a2field_search_order, char* pfield_search_order, char* sefield_search_order, char* essfield_search_order, uint32_t flags, char* extractname, char* outname, char* outname_end, double output_min_p, Chrom_info* chrom_info_ptr);

		#endif // __PLINK_MISC_H__