New upstream version 1.90~b6.15-200121 (223cb97e) · Commits · Debian Med / plink1.9

plink.c

+33 −5

Original line number	Diff line number	Diff line
		// This file is part of PLINK 1.90, copyright (C) 2005-2019 Shaun Purcell,
		// This file is part of PLINK 1.90, copyright (C) 2005-2020 Shaun Purcell,
		// Christopher Chang.
		//
		// This program is free software: you can redistribute it and/or modify
		@@ -93,7 +93,7 @@

		static const char ver_str[] =
		#ifdef STABLE_BUILD
		"PLINK v1.90b6.13"
		"PLINK v1.90b6.15"
		#else
		"PLINK v1.90p"
		#endif
		@@ -105,7 +105,7 @@ static const char ver_str[] =
		#else
		" 32-bit"
		#endif
		" (30 Nov 2019)";
		" (21 Jan 2020)";
		static const char ver_str2[] =
		// include leading space if day < 10, so character length stays the same
		""
		@@ -118,7 +118,7 @@ static const char ver_str2[] =
		" "
		#endif
		" www.cog-genomics.org/plink/1.9/\n"
		"(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3"
		"(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3"
		#if SPECIES_DEFAULT > 0
		"\nRecompiled with default species = "
		#if SPECIES_DEFAULT == SPECIES_COW
		@@ -3163,7 +3163,9 @@ int32_t main(int32_t argc, char** argv) {
		char* gene_report_subset = nullptr;
		char* gene_report_snp_field = nullptr;
		char* metaanal_fnames = nullptr;
		char* metaanal_chrfield_search_order = nullptr;
		char* metaanal_snpfield_search_order = nullptr;
		char* metaanal_bpfield_search_order = nullptr;
		char* metaanal_a1field_search_order = nullptr;
		char* metaanal_a2field_search_order = nullptr;
		char* metaanal_pfield_search_order = nullptr;
		@@ -9457,6 +9459,18 @@ int32_t main(int32_t argc, char** argv) {
		if (retval) {
		goto main_ret_NOMEM;
		}
		} else if (!memcmp(argptr2, "eta-analysis-chr-field", 23)) {
		if (!metaanal_fnames) {
		logerrprint("Error: --meta-analysis-chr-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_chrfield_search_order, &(argv[cur_arg + 1]), param_ct);
		if (retval) {
		goto main_ret_NOMEM;
		}
		} else if (!memcmp(argptr2, "eta-analysis-snp-field", 23)) {
		if (!metaanal_fnames) {
		logerrprint("Error: --meta-analysis-snp-field must be used with --meta-analysis.\n");
		@@ -9469,6 +9483,18 @@ int32_t main(int32_t argc, char** argv) {
		if (retval) {
		goto main_ret_NOMEM;
		}
		} else if (!memcmp(argptr2, "eta-analysis-bp-field", 22)) {
		if (!metaanal_fnames) {
		logerrprint("Error: --meta-analysis-bp-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_bpfield_search_order, &(argv[cur_arg + 1]), param_ct);
		if (retval) {
		goto main_ret_NOMEM;
		}
		} else if (!memcmp(argptr2, "eta-analysis-p-field", 21)) {
		if ((!metaanal_fnames) \|\| (!(metaanal_flags & METAANAL_WEIGHTED_Z))) {
		logerrprint("Error: --meta-analysis-p-field must be used with --meta-analysis + weighted-z.\n");
		@@ -13382,7 +13408,7 @@ 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_sefield_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_chrfield_search_order, metaanal_snpfield_search_order, metaanal_bpfield_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;
		}
		@@ -13643,7 +13669,9 @@ int32_t main(int32_t argc, char** argv) {
		free_cond(gene_report_subset);
		free_cond(gene_report_snp_field);
		free_cond(metaanal_fnames);
		free_cond(metaanal_chrfield_search_order);
		free_cond(metaanal_snpfield_search_order);
		free_cond(metaanal_bpfield_search_order);
		free_cond(metaanal_a1field_search_order);
		free_cond(metaanal_a2field_search_order);
		free_cond(metaanal_pfield_search_order);

plink_assoc.c

+1 −1

Original line number	Diff line number	Diff line
		// This file is part of PLINK 1.90, copyright (C) 2005-2019 Shaun Purcell,
		// This file is part of PLINK 1.90, copyright (C) 2005-2020 Shaun Purcell,
		// Christopher Chang.
		//
		// This program is free software: you can redistribute it and/or modify

plink_assoc.h

+1 −1

Original line number	Diff line number	Diff line
		#ifndef __PLINK_ASSOC_H__
		#define __PLINK_ASSOC_H__

		// This file is part of PLINK 1.90, copyright (C) 2005-2019 Shaun Purcell,
		// This file is part of PLINK 1.90, copyright (C) 2005-2020 Shaun Purcell,
		// Christopher Chang.
		//
		// This program is free software: you can redistribute it and/or modify

plink_calc.c

+1 −1

Original line number	Diff line number	Diff line
		// This file is part of PLINK 1.90, copyright (C) 2005-2019 Shaun Purcell,
		// This file is part of PLINK 1.90, copyright (C) 2005-2020 Shaun Purcell,
		// Christopher Chang.
		//
		// This program is free software: you can redistribute it and/or modify

plink_cluster.c

+1 −1

Original line number	Diff line number	Diff line
		// This file is part of PLINK 1.90, copyright (C) 2005-2019 Shaun Purcell,
		// This file is part of PLINK 1.90, copyright (C) 2005-2020 Shaun Purcell,
		// Christopher Chang.
		//
		// This program is free software: you can redistribute it and/or modify