New upstream version 1.90~b6.5-180913 (0cb99996) · Commits · Debian Med / plink1.9

plink.c

+3 −3

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

		static const char ver_str[] =
		#ifdef STABLE_BUILD
		"PLINK v1.90b6.4"
		"PLINK v1.90b6.5"
		#else
		"PLINK v1.90p"
		#endif
		@@ -105,7 +105,7 @@ static const char ver_str[] =
		#else
		" 32-bit"
		#endif
		" (7 Aug 2018)";
		" (13 Sep 2018)";
		static const char ver_str2[] =
		// include leading space if day < 10, so character length stays the same
		""

plink_calc.c

+1 −1

Original line number	Diff line number	Diff line
		@@ -3028,7 +3028,7 @@ int32_t groupdist_calc(pthread_t* threads, uint32_t unfiltered_sample_ct, uintpt
		dxx = g_reg_tot_x / dww;
		dhh_sd = sqrt((dhh_ssq / dww - dxx * dxx) / (dww - 1.0));
		}
		if (!(g_case_ct * g_ctrl_ct)) {
		if (!(g_case_ct && g_ctrl_ct)) {
		dyy = 0.0;
		dhl_sd = 0.0;
		} else {

plink_data.c

+1 −1

Original line number	Diff line number	Diff line
		@@ -6184,7 +6184,7 @@ int32_t ped_to_bed(char* pedname, char* mapname, char* outname, char* outname_en
		if (bigstack_left() >= marker_ct * sample_ct4) {
		markers_per_pass = marker_ct;
		sprintf(g_logbuf, "Performing single-pass .bed write (%" PRIuPTR " variant%s, %" PRIuPTR " %s).\n", marker_ct, (marker_ct == 1)? "" : "s", sample_ct, species_str(sample_ct));
		pass_ct = (marker_ct * sample_ct4)? 1 : 0;
		pass_ct = (marker_ct && sample_ct4)? 1 : 0;
		} else {
		if (!map_is_unsorted) {
		if (bigstack_alloc_ll(sample_ct, &line_starts)) {

plink_glm.c

+17 −0

Original line number	Diff line number	Diff line
		@@ -1658,12 +1658,29 @@ uint32_t logistic_regression(uint32_t sample_ct, uint32_t param_ct, float* vv, f
		return 1;
		}
		if (iteration >= 15) {
		// quasi-bugfix (11 Sep 2018): if fabsf(any coefficient) > 8e3, this is
		// almost certainly a form of convergence failure that didn't get
		// caught by the (delta_coef > 20.0) check due to a precision quirk.
		// (8e3 threshold ~= 1e-4 * 2^23, since floats have 23 bits of
		// precision)
		for (param_idx = 0; param_idx < param_ct; param_idx++) {
		if (fabsf(coef[param_idx]) > 8e3) {
		return 1;
		}
		}
		return 0;
		}
		}
		// Pons reported that 1.1e-3 was dangerous, so I agree with the decision to
		// tighten this threshold from 1e-3 to 1e-4.
		if (delta_coef < 1e-4) {
		// Be more conservative in throwing out results when we don't hit the
		// iteration limit.
		for (param_idx = 0; param_idx < param_ct; param_idx++) {
		if (fabsf(coef[param_idx]) > 6e4) {
		return 1;
		}
		}
		return 0;
		}
		}

plink_ld.c

+16 −0

Original line number	Diff line number	Diff line
		@@ -3233,6 +3233,7 @@ void fepi_counts_to_joint_effects_stats(uint32_t group_ct, uint32_t* counts, dou
		uint32_t uii;
		uint32_t ujj;
		uint32_t ukk;
		tot_inv_v[0] = 0.0; // gcc7 maybe-uninitialized warning
		dptr = dcounts;
		if (counts[0] && counts[1] && counts[2] && counts[3] && counts[4] && counts[5] && counts[6] && counts[7] && counts[8] && ((group_ct == 1) \|\| (counts[9] && counts[10] && counts[11] && counts[12] && counts[13] && counts[14] && counts[15] && counts[16] && counts[17]))) {
		for (uii = 0; uii < group_ct; uii++) {
		@@ -4712,11 +4713,15 @@ THREAD_RET_TYPE epi_logistic_thread(void* arg) {
		cur_word2 = cur_word2 & (cur_word2 >> 1);
		cur_sample_ct -= popcount2_long((cur_word1 \| cur_word2) & FIVEMASK);
		}
		unsigned char geno_pair_present[12];
		if (cur_sample_ct <= 4) {
		goto epi_logistic_thread_regression_fail;
		}
		// 2. now populate covariate-major matrix with 16-byte-aligned,
		// trailing-entries-zeroed rows
		// quasi-bugfix (13 Sep 2018): reliably detect when this matrix is not
		// of full rank, and skip the regression in that case.
		memset(geno_pair_present, 0, 12);
		cur_sample_cta4 = round_up_pow2(cur_sample_ct, 4);
		for (widx = 0; widx < pheno_nm_ctl2; widx++) {
		sample_idx = widx * BITCT2;
		@@ -4731,6 +4736,7 @@ THREAD_RET_TYPE epi_logistic_thread(void* arg) {
		uljj = cur_word2 & (3 * ONELU);
		if ((ulii != 3) && (uljj != 3)) {
		*fptr = 1.0;
		geno_pair_present[ulii + uljj * 4] = 1;
		fxx = (float)((intptr_t)ulii);
		fyy = (float)((intptr_t)uljj);
		// maybe this is faster with continuous writes instead of
		@@ -4745,6 +4751,16 @@ THREAD_RET_TYPE epi_logistic_thread(void* arg) {
		cur_word2 >>= 2;
		}
		}
		if (!geno_pair_present[5]) {
		// not full rank if any 2x2 square in the 3x3 contingency table is
		// empty.
		if (((!geno_pair_present[0]) && (!geno_pair_present[1]) && (!geno_pair_present[4])) \|\|
		((!geno_pair_present[1]) && (!geno_pair_present[2]) && (!geno_pair_present[6])) \|\|
		((!geno_pair_present[4]) && (!geno_pair_present[8]) && (!geno_pair_present[9])) \|\|
		((!geno_pair_present[6]) && (!geno_pair_present[9]) && (!geno_pair_present[10]))) {
		goto epi_logistic_thread_regression_fail;
		}
		}
		if (cur_sample_ct < cur_sample_cta4) {
		loop_end = cur_sample_cta4 - cur_sample_ct;
		fill_float_zero(loop_end, fptr);