670aea936b66579839b921640e0be7de5985b87b
kent
  Wed Mar 6 14:40:46 2013 -0800
Fixed bug where the empty string was always making it look like one monomer was missing.
diff --git src/kehayden/alphaAsm/alphaAsm.c src/kehayden/alphaAsm/alphaAsm.c
index a697bae..77875ed 100644
--- src/kehayden/alphaAsm/alphaAsm.c
+++ src/kehayden/alphaAsm/alphaAsm.c
@@ -1654,31 +1654,31 @@
 struct monomer *monomer;
 for (monomer = monomerList; monomer != NULL; monomer = monomer->next)
     monomer->outCount = 0;
 
 /* Increase output count each time a monomer is used. */
 struct dlNode *node;
 for (node = ll->head; !dlEnd(node); node = node->next)
     {
     monomer = node->val;
     monomer->outCount += 1;
     }
 
 /* Count up unused. */
 int missing = 0;
 for (monomer = monomerList; monomer != NULL; monomer = monomer->next)
-    if (monomer->outCount == 0)
+    if (monomer->outCount == 0 && !sameString(monomer->word, ""))
         missing += 1;
 
 return missing;
 }
 
 void alphaAsm(char *readsFile, char *monomerOrderFile, char *outFile)
 /* alphaAsm - assemble alpha repeat regions such as centromeres from reads that have
  * been parsed into various repeat monomer variants.  Cycles of these variants tend to
  * form higher order repeats. */
 {
 /* This routine reads in the input,  and then calls a routine that produces the
  * output for a given size.  If not all monomers are included in the output, then it
  * will try to find the minimum output size needed to include all monomers. */
 
 /* Read in inputs, and put in "store" */