9af5c5bbca4f6a2c7d4a4480f87a8fd99b5cc844
hiram
  Tue Feb 19 12:10:30 2013 -0800
add clean makefile target and expand description of ignoreDups usage message
diff --git src/utils/faToTwoBit/faToTwoBit.c src/utils/faToTwoBit/faToTwoBit.c
index 67dd919..e111bdc 100644
--- src/utils/faToTwoBit/faToTwoBit.c
+++ src/utils/faToTwoBit/faToTwoBit.c
@@ -7,31 +7,32 @@
 #include "dnautil.h"
 #include "fa.h"
 #include "twoBit.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faToTwoBit - Convert DNA from fasta to 2bit format\n"
   "usage:\n"
   "   faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit\n"
   "options:\n"
   "   -noMask       - Ignore lower-case masking in fa file.\n"
   "   -stripVersion - Strip off version number after . for genbank accessions.\n"
-  "   -ignoreDups   - only convert first sequence if there are duplicates\n"
+  "   -ignoreDups   - only convert first sequence if there are duplicate sequence\n"
+  "                 - names.  Use 'twoBitDup' to find duplicate sequences."
   );
 }
 
 boolean noMask = FALSE;
 boolean stripVersion = FALSE;
 boolean ignoreDups = FALSE;
 
 static struct optionSpec options[] = {
    {"noMask", OPTION_BOOLEAN},
    {"stripVersion", OPTION_BOOLEAN},
    {"ignoreDups", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 static void unknownToN(char *s, int size)