51aa3926269ede11330a0564c6f67be38b06f825
galt
  Fri Apr 22 12:47:17 2011 -0700
blat segfault fix for maxIntron <= 11 when tileSize <= 11
diff --git src/jkOwnLib/ffAliHelp.c src/jkOwnLib/ffAliHelp.c
index be59241..0ff2dae 100644
--- src/jkOwnLib/ffAliHelp.c
+++ src/jkOwnLib/ffAliHelp.c
@@ -276,45 +276,52 @@
 boolean ffSlideIntrons(struct ffAli *ali)
 /* Slide introns (or spaces between aligned blocks)
  * to match consensus.  Return TRUE if any slid. */
 {
 int orient = ffIntronOrientation(ali);
 return ffSlideOrientedIntrons(ali, orient);
 }
 
 struct ffAli *ffRemoveEmptyAlis(struct ffAli *ali, boolean doFree)
 /* Remove empty blocks from list. Optionally free empties too. */
 {
 struct ffAli *leftAli;
 struct ffAli *startAli;
 struct ffAli *rightAli;
 
+if (ali == NULL)
+    return NULL;
+
 /* Figure out left most non-empty ali. */
 while (ali->left)
     ali = ali->left;
 while (ali)
     {
     /* If current ali is empty, chuck it out. */
     if (ali->nEnd <= ali->nStart || ali->hEnd <= ali->hStart)
 	{
 	struct ffAli *empty = ali;
         ali = ali->right;
 	if (doFree) freeMem(empty);
 	}
     else
         break;
     }
+
+if (ali == NULL)
+    return NULL;
+
 ali->left = NULL;
 
 /* Get rid of empty middle alis. */
 startAli = leftAli = ali;
 ali = ali->right;
 while (ali)
     {
     rightAli = ali->right;
     if (ali->nEnd <= ali->nStart || ali->hEnd <= ali->hStart)
         {
         leftAli->right = rightAli;
         if (rightAli != NULL)
             rightAli->left = leftAli;
 	if (doFree) freeMem(ali);
         }