New upstream version 1.90~b6.2-180612 (9267d062) · Commits · Debian Med / plink1.9

plink.c

+2 −2

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

		static const char ver_str[] =
		#ifdef STABLE_BUILD
		"PLINK v1.90b6.1"
		"PLINK v1.90b6.2"
		#else
		"PLINK v1.90p"
		#endif
		@@ -105,7 +105,7 @@ static const char ver_str[] =
		#else
		" 32-bit"
		#endif
		" (28 May 2018)";
		" (12 Jun 2018)";
		static const char ver_str2[] =
		// include leading space if day < 10, so character length stays the same
		""

plink_assoc.c

+69 −46

Original line number	Diff line number	Diff line
		@@ -2379,16 +2379,16 @@ THREAD_RET_TYPE assoc_adapt_thread(void* arg) {
		gpui = &(precomp_ui[4 * precomp_width * marker_bidx]);
		success_2start = perm_2success_ct[marker_idx];
		success_2incr = 0;
		if (model_fisher) {
		stat_high = orig_pvals[marker_idx] * (1.0 + EPSILON);
		stat_low = orig_pvals[marker_idx] * (1.0 - EPSILON);
		} else {
		if (orig_pvals[marker_idx] == -9) {
		perm_adapt_stop[marker_idx] = 1;
		perm_attempt_ct[marker_idx] = next_adapt_check;
		perm_2success_ct[marker_idx] = next_adapt_check;
		continue;
		}
		if (model_fisher) {
		stat_high = orig_pvals[marker_idx] * (1.0 + EPSILON);
		stat_low = orig_pvals[marker_idx] * (1.0 - EPSILON);
		} else {
		stat_high = orig_chisq[marker_idx] + EPSILON;
		stat_low = orig_chisq[marker_idx] - EPSILON;
		}
		@@ -2582,11 +2582,7 @@ THREAD_RET_TYPE assoc_maxt_thread(void* arg) {
		msa_ptr = &(mperm_save_all[marker_idx * perm_vec_ct]);
		}
		for (; marker_bidx < marker_bceil; marker_bidx++) {
		if (model_fisher) {
		stat_high = orig_pvals[marker_idx] * (1.0 + EPSILON);
		stat_low = orig_pvals[marker_idx] * (1.0 - EPSILON);
		} else {
		if (g_orig_pvals[marker_idx] == -9) {
		if (orig_pvals[marker_idx] == -9) {
		if (msa_ptr) {
		for (pidx = 0; pidx < perm_vec_ct; pidx++) {
		*msa_ptr++ = -9;
		@@ -2595,6 +2591,10 @@ THREAD_RET_TYPE assoc_maxt_thread(void* arg) {
		perm_2success_ct[marker_idx++] += perm_vec_ct;
		continue;
		}
		if (model_fisher) {
		stat_high = orig_pvals[marker_idx] * (1.0 + EPSILON);
		stat_low = orig_pvals[marker_idx] * (1.0 - EPSILON);
		} else {
		stat_high = orig_chisq[marker_idx] + EPSILON;
		stat_low = orig_chisq[marker_idx] - EPSILON;
		}
		@@ -5001,6 +5001,11 @@ THREAD_RET_TYPE model_adapt_best_thread(void* arg) {
		for (; marker_bidx < marker_bceil; marker_bidx++) {
		marker_idx = g_adapt_m_table[marker_bidx];
		if (model_fisher) {
		if (orig_pvals[marker_idx] == -9) {
		perm_adapt_stop[marker_idx] = 1;
		perm_attempt_ct[marker_idx] = 0;
		continue;
		}
		stat_high = orig_pvals[marker_idx] * (1.0 + EPSILON);
		stat_low = orig_pvals[marker_idx] * (1.0 - EPSILON);
		} else {
		@@ -5263,6 +5268,10 @@ THREAD_RET_TYPE model_maxt_best_thread(void* arg) {
		}
		for (; marker_bidx < marker_bceil; marker_bidx++) {
		if (model_fisher) {
		if (orig_pvals[marker_idx] == -9) {
		marker_idx++;
		continue;
		}
		stat_high = orig_pvals[marker_idx] * (1.0 + EPSILON);
		stat_low = orig_pvals[marker_idx] * (1.0 - EPSILON);
		default_best_stat = 1;
		@@ -6751,23 +6760,33 @@ int32_t model_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, cha
		du1 = ujj;
		du2 = uii;
		if (model_fisher) {
		// bugfix (12 Jun 2018): If MAF is zero, test should not be
		// considered valid for --adjust or permutation testing purposes.
		// plink 1.07 got this right, but in a wrong way: it considered
		// all Fisher's-exact-test p-values of 1 to be invalid tests. So
		// we don't generally want to match its output (even before
		// considering the problems with its fisher22 routine).
		if ((umm + ujj) && (ukk + uii)) {
		pval = fisher22(uii, ujj, ukk, umm, fisher_midp);
		*orig_pvals_ptr = pval;
		} else {
		if ((!umm) && (!ujj)) {
		*orig_pvals_ptr = -9;
		pval = -1;
		dxx = 0;
		if (fill_orig_chisq) {
		orig_chisq[marker_idx + marker_bidx] = -9;
		pval = -9;
		}
		*orig_pvals_ptr = pval;
		} else {
		if ((umm + ujj) && (ukk + uii)) {
		dxx = chi22_eval(ukk, ukk + umm, uii + ukk, uii + ujj + ukk + umm);
		pval = chiprob_p(dxx, 1);
		*orig_pvals_ptr = pval;
		if (fill_orig_chisq) {
		orig_chisq[marker_idx + marker_bidx] = dxx;
		}
		} else {
		*orig_pvals_ptr = -9;
		pval = -1;
		dxx = 0;
		if (fill_orig_chisq) {
		orig_chisq[marker_idx + marker_bidx] = -9;
		}
		}
		}
		ooptr = (da1 du2) / (du1 * da2);
		@@ -6803,7 +6822,11 @@ int32_t model_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, cha
		wptr = fw_strcpy(4, a2ptr, &(wptr[1]));
		*wptr++ = ' ';
		if (model_fisher) {
		if (pval == -9) {
		wptr = memcpya(wptr, " 1", 12);
		} else {
		wptr = dtoa_g_wxp4(MAXV(pval, output_min_p), 12, wptr);
		}
		} else {
		if (pval > -1) {
		wptr = dtoa_g_wxp4x(dxx, 12, ' ', wptr);