debian/changelog

+plink1.9 (1.90~b6.2-180612-1) unstable; urgency=medium
+
+  * New upstream release.
+
+ -- Dylan Aïssi <bob.dybian@gmail.com>  Wed, 04 Jul 2018 22:13:26 +0200
+
 plink1.9 (1.90~b6.1-180528-1) unstable; urgency=medium
 
   * New upstream release.

debian/upstream.docs/upstream.changelog

 # Copy/Paste from https://www.cog-genomics.org/plink/1.9/
 
-28 May 2018: Fixed --file triallelic-variant handling bug which occurred when the .map was unsorted.
+12 Jun 2018: "--assoc fisher"'s multiple testing corrections no longer treat zero-MAF variants as valid tests.
+
+28 May: Fixed --file triallelic-variant handling bug which occurred when the .map was unsorted.
 
 26 May (beta 6): --merge-equal-pos bugfixes. If you used --merge-equal-pos with .bed+.bim+.fam filesets where allele order may have differed between .bim files, or with any .ped+.map fileset at all, we recommend redoing that run.
 

plink.c

@@ -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

@@ -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);