1 files changed, 103 insertions, 0 deletions
diff --git a/academic/wise/patches/08_mayhem.patch b/academic/wise/patches/08_mayhem.patch
new file mode 100644
index 0000000000..c54c7c66ab
--- /dev/null
+++ b/academic/wise/patches/08_mayhem.patch
@@ -0,0 +1,103 @@
+Author: Philipp Benner <philipp@debian.org>
+Last-Update: Sun, 07 Jul 2013 13:33:01 +0200
+Description: Fix run time errors detected by Mayhem
+
+--- wise-2.4.1.orig/src/models/dbac.c
++++ wise-2.4.1/src/models/dbac.c
+@@ -535,8 +535,12 @@
+    *  
+    */  
+   
+-  one = read_fasta_file_Sequence(*argv++);  
+-  two = read_fasta_file_Sequence(*argv++);  
++  if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) {
++    fatal("Unable to read the sequence in file");
++  }
++  if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) {
++    fatal("Unable to read the sequence in file");
++  }
+   
+   uppercase_Sequence(one);  
+   uppercase_Sequence(two);  
+--- wise-2.4.1.orig/src/models/estwise.c
++++ wise-2.4.1/src/models/estwise.c
+@@ -313,7 +313,7 @@
+     }
+   }
+ 
+-  if( reverse == TRUE ) {
++  if( cdna && reverse == TRUE ) {
+     if( tstart > tend ) {
+       warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend);
+     }
+@@ -323,7 +323,7 @@
+     cdna = cdna_temp;
+   }
+ 
+-  if( target_abs == TRUE ) {
++  if( cdna && target_abs == TRUE ) {
+     cdna->baseseq->offset = 1;
+     cdna->baseseq->end  = strlen(cdna->baseseq->seq);
+   }
+@@ -472,8 +472,11 @@
+   }
+ 
+   cp = flat_cDNAParser(indel_error);
+-  cm = flat_CodonMapper(ct);
+-  sprinkle_errors_over_CodonMapper(cm,subs_error);
++
++  if( ct ) {
++    cm = flat_CodonMapper(ct);
++    sprinkle_errors_over_CodonMapper(cm,subs_error);
++  }
+ 
+   return ret;
+ 
+--- wise-2.4.1.orig/src/models/genewise.c
++++ wise-2.4.1/src/models/genewise.c
+@@ -550,8 +550,10 @@
+       ret =  FALSE;
+     }
+ 
+-    gen->baseseq->offset = 1;
+-    gen->baseseq->end  = strlen(gen->baseseq->seq);
++    if ( gen ) {
++      gen->baseseq->offset = 1;
++      gen->baseseq->end  = strlen(gen->baseseq->seq);
++    }
+   }
+ 
+   if( alg_str != NULL ) {
+--- wise-2.4.1.orig/src/models/estwisedb.c
++++ wise-2.4.1/src/models/estwisedb.c
+@@ -688,8 +688,11 @@
+ 
+ 
+   cps = flat_cDNAParser(indel_error);
+-  cm = flat_CodonMapper(ct);
+-  sprinkle_errors_over_CodonMapper(cm,subs_error);
++
++  if( ct ) {
++    cm = flat_CodonMapper(ct);
++    sprinkle_errors_over_CodonMapper(cm,subs_error);
++  }
+ 
+   return ret;
+ 
+--- wise-2.4.1.orig/src/models/promoterwise.c
++++ wise-2.4.1/src/models/promoterwise.c
+@@ -147,8 +147,12 @@
+ 
+   lchs = standard_LocalCisHitScore(NMaskType_VARIABLE);
+ 
+-  query = read_fasta_file_Sequence(argv[1]);
+-  target = read_fasta_file_Sequence(argv[2]);
++  if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) {
++    fatal("Unable to read the sequence in query file");
++  }
++  if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) {
++    fatal("Unable to read the sequence in target file");
++  }
+ 
+   for(i=0;i<query->len;i++) {
+     query->seq[i] = toupper(query->seq[i]);