debian/changelog

+plink1.9 (1.90~b6.4-180807-1) unstable; urgency=medium
+
+  * New upstream release.
+
+ -- Dylan Aïssi <bob.dybian@gmail.com>  Wed, 22 Aug 2018 18:11:44 +0200
+
 plink1.9 (1.90~b6.3-180717-1) unstable; urgency=medium
 
   * New upstream release.

debian/upstream.docs/upstream.changelog

 # Copy/Paste from https://www.cog-genomics.org/plink/1.9/
 
-17 Jul 2018: Fixed uninitialized --make-set-border value bug.
+7 Aug 2018: --assoc set-test bugfix.
+
+17 Jul: Fixed uninitialized --make-set-border value bug.
 
 12 Jun: "--assoc fisher"'s multiple testing corrections no longer treat zero-MAF variants as valid tests.
 

plink.c

@@ -93,7 +93,7 @@
 static const char ver_str[] =
 #ifdef STABLE_BUILD
-  "PLINK v1.90b6.3"
+  "PLINK v1.90b6.4"
 #else
   "PLINK v1.90p"
 #endif
@@ -105,7 +105,7 @@ static const char ver_str[] =
 #else
   " 32-bit"
 #endif
-  " (17 Jul 2018)";
+  " (7 Aug 2018)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   " "

plink_assoc.c

@@ -5918,6 +5918,8 @@ int32_t model_assoc_set_test(pthread_t* threads, FILE* bedfile, uintptr_t bed_of
 	}
 	goto model_assoc_set_test_perms_done;
       }
+      // bugfix (7 Aug 2018): forgot to update marker_unstopped_ct
+      marker_unstopped_ct = popcount_longs(unstopped_markers, (marker_ct + BITCT - 1) / BITCT);
     }
     printf("\r%u permutation%s complete.", perms_done, (perms_done != 1)? "s" : "");
     fflush(stdout);