gentoo-overlay/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch

--- a/doc/release-notes.html
+++ b/doc/release-notes.html
@@ -15,6 +15,21 @@
     </div>
     <h2>MEME Suite Release Notes</h2>
     <hr>
+      <b>MEME version 4.11.2 patch 2 -- October 24, 2016</b>
+      <ul>
+        <li>
+            <b>Bug fixes</b>
+            <ul>
+              <li>
+              Fixed bug in handling of RNA-like custom alphabets.
+              </li>
+              <li>
+              Fixed bug in MAST -comp option.
+              </li>
+            </ul
+        </li>
+      </ul>
+      <hr>
       <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
       <ul>
         <li>
--- a/src/alph-in.c
+++ b/src/alph-in.c
@@ -1044,7 +1044,7 @@
           lookup[0] = sym->complement;
           comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup);
         }
-        if (comp1 != comp2) {
+        if (comp1 && (comp1 != comp2)) {
           add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1, 
                 "not like %s alphabet as %c complement rules are incorrect",
                 ext_name, req_syms[i]));
--- a/src/mast-util.c
+++ b/src/mast-util.c
@@ -740,14 +740,14 @@
 
   // create the frequency array  
   alph = xlate ? xlate_dest_alph(xlate) : alph;
-  freq = allocate_array(alph_size_core(alph));
+  freq = allocate_array(alph_size_full(alph));
   init_array(0, freq);
 
   // count the number of letters of each type 
   if (xlate) {
     for (n=0; sequence[n]; n++) {
       i = xlate_index(xlate, false, sequence+n);
-      if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq);
+      if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq);
     }
   } else {
     for (n=0; sequence[n]; n++) {