New upstream version 1.90~b6.13-191130 (152a5d35) · Commits · Debian Med / plink1.9

plink.c

+16 −16

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

		static const char ver_str[] =
		#ifdef STABLE_BUILD
		"PLINK v1.90b6.12"
		"PLINK v1.90b6.13"
		#else
		"PLINK v1.90p"
		#endif
		@@ -105,7 +105,7 @@ static const char ver_str[] =
		#else
		" 32-bit"
		#endif
		" (28 Oct 2019)";
		" (30 Nov 2019)";
		static const char ver_str2[] =
		// include leading space if day < 10, so character length stays the same
		""
		@@ -4720,7 +4720,7 @@ int32_t main(int32_t argc, char** argv) {
		for (uii = 1; uii <= param_ct; uii++) {
		if (!strcmp(argv[cur_arg + uii], "perm")) {
		if (cluster.modifier & CLUSTER_CMH_MPERM) {
		logerrprint("Error: --bd 'mperm' and 'perm{,-bd}' cannot be used together.\n");
		logerrprint("Error: --bd 'mperm' and 'perm[-bd]' cannot be used together.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if (cluster.modifier & CLUSTER_CMH_PERM_BD) {
		logerrprint("Error: --bd 'perm' and 'perm-bd' modifiers cannot be used together.\n");
		@@ -4729,7 +4729,7 @@ int32_t main(int32_t argc, char** argv) {
		cluster.modifier \|= CLUSTER_CMH_PERM;
		} else if (!strcmp(argv[cur_arg + uii], "perm-bd")) {
		if (cluster.modifier & CLUSTER_CMH_MPERM) {
		logerrprint("Error: --bd 'mperm' and 'perm{,-bd}' cannot be used together.\n");
		logerrprint("Error: --bd 'mperm' and 'perm[-bd]' cannot be used together.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if ((cluster.modifier & (CLUSTER_CMH_PERM \| CLUSTER_CMH_PERM_BD)) == CLUSTER_CMH_PERM) {
		logerrprint("Error: --bd 'perm' and 'perm-bd' modifiers cannot be used together.\n");
		@@ -4741,7 +4741,7 @@ int32_t main(int32_t argc, char** argv) {
		cluster.modifier \|= CLUSTER_CMH_PERM_BD;
		} else if ((strlen(argv[cur_arg + uii]) > 6) && (!memcmp(argv[cur_arg + uii], "mperm=", 6))) {
		if (cluster.modifier & CLUSTER_CMH_PERM) {
		logerrprint("Error: --bd 'mperm' and 'perm{,-bd}' cannot be used together.\n");
		logerrprint("Error: --bd 'mperm' and 'perm[-bd]' cannot be used together.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if (cluster.modifier & CLUSTER_CMH_MPERM) {
		logerrprint("Error: Duplicate --bd 'mperm' modifier.\n");
		@@ -4959,7 +4959,7 @@ int32_t main(int32_t argc, char** argv) {
		case 'c':
		if (!memcmp(argptr2, "hr", 3)) {
		if (chrom_flag_present) {
		logerrprint("Error: --chr cannot be used with --autosome{,-xy}.\n");
		logerrprint("Error: --chr cannot be used with --autosome[-xy].\n");
		goto main_ret_INVALID_CMDLINE_A;
		}
		retval = parse_chrom_ranges(param_ct, '-', &(argv[cur_arg]), chrom_info.chrom_mask, &chrom_info, (misc_flags / MISC_ALLOW_EXTRA_CHROMS) & 1, argptr);
		@@ -6680,7 +6680,7 @@ int32_t main(int32_t argc, char** argv) {
		misc_flags \|= MISC_FREQX;
		} else if (!memcmp(argptr2, "rom", 4)) {
		if (chrom_flag_present) {
		logerrprint("Error: --from cannot be used with --autosome{,-xy} or --{,not-}chr.\n");
		logerrprint("Error: --from cannot be used with --autosome[-xy] or --[not-]chr.\n");
		goto main_ret_INVALID_CMDLINE_A;
		}
		if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 1)) {
		@@ -9593,7 +9593,7 @@ int32_t main(int32_t argc, char** argv) {
		calculation_type \|= CALC_NEIGHBOR;
		} else if (!memcmp(argptr2, "ot-chr", 7)) {
		if (markername_from) {
		logerrprint("Error: --from cannot be used with --autosome{,-xy} or --{,not-}chr.\n");
		logerrprint("Error: --from cannot be used with --autosome[-xy] or --[not-]chr.\n");
		goto main_ret_INVALID_CMDLINE_A;
		}
		// allowed:
		@@ -9603,7 +9603,7 @@ int32_t main(int32_t argc, char** argv) {
		// does not make sense, disallowed:
		// --allow-extra-chr --chr 5-22 --not-chr bobs_chrom

		// --allow-extra-chr present, --chr/--autosome{,-xy} not present
		// --allow-extra-chr present, --chr/--autosome[-xy] not present
		uii = ((misc_flags / MISC_ALLOW_EXTRA_CHROMS) & 1) && (!chrom_info.is_include_stack);
		retval = parse_chrom_ranges(param_ct, '-', &(argv[cur_arg]), chrom_exclude, &chrom_info, uii, argptr);
		if (retval) {
		@@ -9870,13 +9870,13 @@ int32_t main(int32_t argc, char** argv) {
		logerrprint("Error: --parallel cannot be used with \"--distance square\". Use \"--distance\nsquare0\" or plain --distance instead.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if ((dist_calc_type & (DISTANCE_BIN \| DISTANCE_BIN4)) && (!(dist_calc_type & DISTANCE_SHAPEMASK))) {
		logerrprint("Error: --parallel cannot be used with plain \"--distance bin{,4}\". Use e.g.\n\"--distance bin square0\" or \"--distance bin triangle\" instead.\n");
		logerrprint("Error: --parallel cannot be used with plain \"--distance bin[4]\". Use e.g.\n\"--distance bin square0\" or \"--distance bin triangle\" instead.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if ((rel_info.modifier & REL_CALC_SHAPEMASK) == REL_CALC_SQ) {
		logerrprint("Error: --parallel cannot be used with \"--make-rel square\". Use \"--make-rel\nsquare0\" or plain --make-rel instead.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if ((rel_info.modifier & (REL_CALC_BIN \| REL_CALC_BIN4)) && (!(rel_info.modifier & (REL_CALC_SHAPEMASK \| REL_CALC_GRM_BIN)))) {
		logerrprint("Error: --parallel cannot be used with plain \"--make-rel bin{,4}\". Use e.g.\n\"--make-rel bin square0\" or \"--make-rel bin triangle\" instead.\n");
		logerrprint("Error: --parallel cannot be used with plain \"--make-rel bin[4]\". Use e.g.\n\"--make-rel bin square0\" or \"--make-rel bin triangle\" instead.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if (calculation_type & CALC_PLINK1_DISTANCE_MATRIX) {
		logerrprint("Error: --parallel and --distance-matrix cannot be used together. Use\n--distance instead.\n");
		@@ -10828,7 +10828,7 @@ int32_t main(int32_t argc, char** argv) {
		logerrprint("Error: Conflicting --r/--r2 modifiers.\n");
		goto main_ret_INVALID_CMDLINE;
		} else if (ld_info.modifier & LD_MATRIX_SPACES) {
		logerrprint("Error: --r/--r2 'bin{,4}' and 'spaces' modifiers cannot be used together.\n");
		logerrprint("Error: --r/--r2 'bin[4]' and 'spaces' modifiers cannot be used together.\n");
		goto main_ret_INVALID_CMDLINE;
		}
		ld_info.modifier \|= LD_MATRIX_BIN;
		@@ -10839,7 +10839,7 @@ int32_t main(int32_t argc, char** argv) {
		logerrprint("Error: Conflicting --r/--r2 modifiers.\n");
		goto main_ret_INVALID_CMDLINE;
		} else if (ld_info.modifier & LD_MATRIX_SPACES) {
		logerrprint("Error: --r/--r2 'bin{,4}' and 'spaces' modifiers cannot be used together.\n");
		logerrprint("Error: --r/--r2 'bin[4]' and 'spaces' modifiers cannot be used together.\n");
		goto main_ret_INVALID_CMDLINE;
		}
		ld_info.modifier \|= LD_MATRIX_BIN4;
		@@ -10850,7 +10850,7 @@ int32_t main(int32_t argc, char** argv) {
		if (ld_info.modifier & (LD_INTER_CHR \| LD_INPHASE \| LD_DX \| LD_WITH_FREQS)) {
		goto main_r2_matrix_conflict;
		} else if (ld_info.modifier & (LD_MATRIX_BIN \| LD_MATRIX_BIN4)) {
		logerrprint("Error: --r/--r2 'bin{,4}' and 'spaces' modifiers cannot be used together.\n");
		logerrprint("Error: --r/--r2 'bin[4]' and 'spaces' modifiers cannot be used together.\n");
		goto main_ret_INVALID_CMDLINE;
		}
		ld_info.modifier \|= LD_MATRIX_SPACES;
		@@ -10974,7 +10974,7 @@ int32_t main(int32_t argc, char** argv) {
		logerrprint("Error: --snp cannot be used with --from-bp/-kb/-mb.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if ((!are_all_words_zero(chrom_info.chrom_mask, CHROM_MASK_INITIAL_WORDS)) \|\| chrom_info.incl_excl_name_stack) {
		logerrprint("Error: --snp cannot be used with --autosome{,-xy} or --{,not-}chr.\n");
		logerrprint("Error: --snp cannot be used with --autosome[-xy] or --[not-]chr.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if (markername_snp) {
		logerrprint("Error: --snp cannot be used with --exclude-snp.\n");
		@@ -11704,7 +11704,7 @@ int32_t main(int32_t argc, char** argv) {
		load_rare \|= LOAD_RARE_TPED;
		} else if (!memcmp(argptr2, "o", 2)) {
		if ((!are_all_words_zero(chrom_info.chrom_mask, CHROM_MASK_INITIAL_WORDS)) \|\| chrom_info.incl_excl_name_stack) {
		logerrprint("Error: --to cannot be used with --autosome{,-xy} or --{,not-}chr.\n");
		logerrprint("Error: --to cannot be used with --autosome[-xy] or --[not-]chr.\n");
		goto main_ret_INVALID_CMDLINE_A;
		} else if (markername_snp) {
		logerrprint("Error: --to cannot be used with --snp.\n");

plink_data.c

+1 −1

Original line number	Diff line number	Diff line
		@@ -14221,7 +14221,7 @@ int32_t recode(uint32_t recode_modifier, FILE* bedfile, uintptr_t bed_offset, ch
		}

		// bugfix: stop generating a .map file when Oxford-format requested
		if (recode_modifier & (RECODE_COMPOUND \| RECODE_LGEN \| RECODE_LGEN_REF \| RECODE_PED)) {
		if (recode_modifier & (RECODE_COMPOUND \| RECODE_LGEN \| RECODE_LGEN_REF \| RECODE_PED \| RECODE_RLIST)) {
		strcpy(outname_end, ".map");
		retval = write_map_or_bim(outname, marker_exclude, marker_ct, marker_ids, max_marker_id_len, marker_cms, marker_pos, nullptr, ((recode_modifier & (RECODE_TAB \| RECODE_DELIMX)) == RECODE_DELIMX)? ' ' : '\t', chrom_info_ptr);
		if (retval) {

plink_help.c

+9 −9

Original line number	Diff line number	Diff line
		@@ -833,9 +833,9 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		" * If you're satisfied with all the default settings described below, just\n"
		" use --homozyg with no modifiers. Otherwise, --homozyg lets you change a\n"
		" few binary settings:\n"
		" * 'group{,-verbose}' adds a report on pools of overlapping runs of\n"
		" * 'group[-verbose]' adds a report on pools of overlapping runs of\n"
		" homozygosity. (Automatically set when --homozyg-match is present.)\n"
		" * With 'group{,-verbose}', 'consensus-match' causes pairwise segmental\n"
		" * With 'group[-verbose]', 'consensus-match' causes pairwise segmental\n"
		" matches to be called based on the variants in the pool's consensus\n"
		" segment, rather than the variants in the pairwise intersection.\n"
		" * Due to how the scanning window algorithm works, it is possible for a\n"
		@@ -1253,7 +1253,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		" * 'nop' strips p-values from the main report.\n"
		" * These computations can be subdivided with --parallel; however...\n"
		" --epistasis-summary-merge <common file prefix> <ct>\n"
		" When a --{,fast-}epistasis job is subdivided with --parallel, the main\n"
		" When a --[fast-]epistasis job is subdivided with --parallel, the main\n"
		" report can be assembled at the end by applying Unix 'cat' in the usual\n"
		" manner, but the .summary.1, .summary.2, ... files may require a specialized\n"
		" merge. --epistasis-summary-merge takes care of the latter.\n\n"
		@@ -1407,8 +1407,8 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		" --simulate-n <num> : Set --simulate-qt sample count (default 1000).\n"
		);
		help_print("simulate\tsimulate-qt\tsimulate-label\tsimulate-missing", &help_ctrl, 0,
		" --simulate-label <prefix> : Set --simulate{,-qt} FID/IID name prefix.\n"
		" --simulate-missing <freq> : Set --simulate{,-qt} missing genotype frequency.\n"
		" --simulate-label <prefix> : Set --simulate[-qt] FID/IID name prefix.\n"
		" --simulate-missing <freq> : Set --simulate[-qt] missing genotype frequency.\n"
		);
		help_print("allow-extra-chr\taec", &help_ctrl, 0,
		" --allow-extra-chr ['0'] : Permit unrecognized chromosome codes. The '0'\n"
		@@ -1638,7 +1638,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		);
		help_print("read-freq\tupdate-freq", &help_ctrl, 0,
		" --read-freq <fn> : Estimate MAFs and heterozygote frequencies from the given\n"
		" --freq{,x} report, instead of the input fileset.\n"
		" --freq[x] report, instead of the input fileset.\n"
		);
		help_print("hwe\thwe-all\thwe2", &help_ctrl, 0,
		" --hwe <p> ['midp'] ['include-nonctrl'] : Exclude variants with Hardy-Weinberg\n"
		@@ -1813,7 +1813,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		" covariate file.\n"
		);
		help_print("merge\tbmerge\tmerge-list\tmerge-mode", &help_ctrl, 0,
		" --merge-mode <n> : Adjust --{,b}merge/--merge-list behavior based on a\n"
		" --merge-mode <n> : Adjust --[b]merge/--merge-list behavior based on a\n"
		" numeric code.\n"
		" 1 (default) = ignore missing calls, otherwise difference\n"
		" -> missing\n"
		@@ -1853,7 +1853,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		" --tag-mode2 : Use two-column --show-tags (file mode) I/O format.\n"
		);
		help_print("indep\tindep-pairwise\tr\tr2\tflip-scan\tflipscan\tshow-tags\tld-xchr", &help_ctrl, 0,
		" --ld-xchr <code> : Set chrX model for --indep{,-pairwise}, --r/--r2,\n"
		" --ld-xchr <code> : Set chrX model for --indep[-pairwise], --r/--r2,\n"
		" --flip-scan, and --show-tags.\n"
		" 1 (default) = males coded 0/1, females 0/1/2 (A1 dosage)\n"
		" 2 = males coded 0/2\n"
		@@ -2090,7 +2090,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
		);
		help_print("fast-epistasis\tepistasis\tgap\tepi1\tepi2", &help_ctrl, 0,
		" --gap <kbs> : Set \"--fast-epistasis case-only\" min. gap (default 1000).\n"
		" --epi1 <p-value> : Set --{,fast-}epistasis reporting threshold (default\n"
		" --epi1 <p-value> : Set --[fast-]epistasis reporting threshold (default\n"
		" 5e-6 for 'boost', 1e-4 otherwise).\n"
		" --epi2 <p-value> : Set threshold for contributing to SIG_E count (def. 0.01).\n"
		);