debian/changelog

+plink1.9 (1.90~b5.3-180221-1) unstable; urgency=medium
+
+  * New upstream release.
+
+ -- Dylan Aïssi <bob.dybian@gmail.com>  Thu, 08 Mar 2018 21:50:36 +0100
+
 plink1.9 (1.90~b5.2-180109-1) unstable; urgency=medium
 
   * New upstream release.

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Dylan Aïssi <bob.dybian@gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11),
+Build-Depends: debhelper (>= 11~),
                help2man,
                libatlas-base-dev,
                liblapack-dev,

debian/upstream.docs/upstream.changelog

 # Copy/Paste from https://www.cog-genomics.org/plink/1.9/
 
+21 Feb 2018: "--indiv-sort file" no longer scrambles the phenotypes when used with --{b}merge or --merge-list.
+
 9 Jan 2018: --all-pheno no longer gets into an infinite loop when one phenotype is all-missing.
 
 20 Dec 2017: --meta-analysis 'report-all' now reports original stats instead of 'NA' when N=1. Fixed an inaccuracy in --adjust's handling of very small p-values. --make-just-fam works properly with just .fam input again.

plink.c

@@ -93,7 +93,7 @@
 static const char ver_str[] =
 #ifdef STABLE_BUILD
-  "PLINK v1.90b5.2"
+  "PLINK v1.90b5.3"
 #else
   "PLINK v1.90p"
 #endif
@@ -105,7 +105,7 @@ static const char ver_str[] =
 #else
   " 32-bit"
 #endif
-  " (9 Jan 2018)";
+  " (21 Feb 2018)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""

plink_data.c

@@ -16284,10 +16284,12 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam
 	  goto merge_datasets_ret_WRITE_FAIL;
 	}
 	if (is_dichot_pheno) {
-	  cc = pheno_c_char[ulii];
+          // bugfix (21 Feb 2018): need to use the map_reverse index here,
+          // since the phenotypes correspond to ASCII-sorted sample ID order.
+	  cc = pheno_c_char[ujj];
 	  fprintf(outfile, "\t%s\n", cc? ((cc == 1)? "2" : "-9") : "1");
 	} else {
-	  fprintf(outfile, "\t%g\n", pheno_d[ulii]);
+	  fprintf(outfile, "\t%g\n", pheno_d[ujj]);
 	}
       }
     }