Index: src/utils/faCmp/faCmp.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/faCmp/faCmp.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 4 -r1.7 -r1.8
--- src/utils/faCmp/faCmp.c	30 Jan 2008 23:11:27 -0000	1.7
+++ src/utils/faCmp/faCmp.c	13 Nov 2009 21:33:25 -0000	1.8
@@ -23,8 +23,14 @@
   "    -peptide - read as peptide sequences\n"
   "default:\n"
   "    no masking information is used during compare.  It is as if both\n"
   "    sequences were not masked.\n"
+  "\n"
+  "Exit codes:\n"
+  "   - 0 if files are the same\n"
+  "   - 1 if files differ\n"
+  "   - 255 on an error\n"
+  "\n"
   );
 }
 /* command line options and values */
 static struct optionSpec optionSpecs[] =
@@ -81,9 +87,12 @@
     slSort(&bList, faSortByName);
     }
 
 if (aCount != bCount)
-   errAbort("%d sequences in %s, %d in %s", aCount, aFile, bCount, bFile);
+    {
+    fprintf(stderr, "%d sequences in %s, %d in %s\n", aCount, aFile, bCount, bFile);
+    exit(1);
+    }
 for (a = aList, b = bList; a != NULL && b != NULL; a = a->next, b = b->next)
     {
     verbose(2, "comparing %s to %s\n",a->name, b->name);
     if (a->size != b->size)
@@ -109,9 +118,12 @@
     }
 if (errCount == 0)
     fprintf(stderr, "%s and %s are the same\n", aFile, bFile);
 else
-    errAbort("%s and %s have %d sequences that differ", aFile, bFile, errCount);
+    {
+    fprintf(stderr, "%s and %s have %d sequences that differ\n", aFile, bFile, errCount);
+    exit(1);
+    }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */

