debian/changelog

+examl (3.0.21-1) unstable; urgency=medium
+
+  * New upstream version
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Fri, 08 Jun 2018 13:10:46 +0200
+
 examl (3.0.20-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -5,9 +5,9 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                libopenmpi-dev
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/examl.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/examl.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/examl
+Vcs-Git: https://salsa.debian.org/med-team/examl.git
 Homepage: https://github.com/stamatak/ExaML
 
 Package: examl

parser/parsePartitions.c

@@ -370,7 +370,15 @@ static int myGetline(char **lineptr, int *n, FILE *stream)
   return p - *lineptr;
 }
 
-
+static void nonContiguousError(analdef *adef)
+{
+  if(adef->compressPatterns == FALSE)
+    {
+      printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n");
+      printf("to the same partition model, when pattern compression is disabled via the -c flag!\n\n");
+      exit(-1);
+    }
+}
 
 void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
 {
@@ -499,6 +507,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
       if(*ch == ',')
 	{	     
 	  upper = lower;
+	  nonContiguousError(adef);
 	  goto SINGLE_NUMBER;
 	}
       
@@ -542,6 +551,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
       if(*ch == ',')
 	{	 
 	  ch++;
+	  nonContiguousError(adef);
 	  goto numberPairs;
 	}
       
@@ -556,12 +566,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
 	      exit(-1);
 	    }   
 
-	  if(adef->compressPatterns == FALSE)
-	    {
-	      printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n");
-	      printf("to the same partition model, when pattern compression is disabled via the -c flag!\n\n");
-	      exit(-1);
-	    }
+	  nonContiguousError(adef);
 
 	  l = 0;
 	  while(isNum(*ch))
@@ -582,6 +587,7 @@ void parsePartitions(analdef *adef, rawdata *rdta, tree *tr)
 	  if(*ch == ',')
 	    {	       
 	      ch++;
+	      nonContiguousError(adef);
 	      goto numberPairs;
 	    }
 	}  

versionHeader/version.h

 #define programName        "ExaML"
-#define programVersion     "3.0.20"
-#define programVersionInt  3020
-#define programDate        "January 26 2018"
+#define programVersion     "3.0.21"
+#define programVersionInt  3021
+#define programDate        "May 29 2018"