265c822fad7002219f5639b8bd3c7f40a9445188
kent
  Tue Sep 11 11:15:14 2012 -0700
Removing pairFile command line parameter since not yet using it.  Improving usage message.
diff --git src/kehayden/alphaChain/alphaChain.c src/kehayden/alphaChain/alphaChain.c
index 3414909..16cd7e9 100644
--- src/kehayden/alphaChain/alphaChain.c
+++ src/kehayden/alphaChain/alphaChain.c
@@ -7,31 +7,37 @@
 #include "dystring.h"
 #include "dlist.h"
 
 /* Global vars - all of which can be set by command line options. */
 int maxChainSize = 3;
 int outSize = 10000;
 boolean fullOnly = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "alphaChain - create a linear projection of alpha satellite arrays using the probablistic model\n"
   "of HuRef satellite graphs\n"
   "usage:\n"
-  "   alphaChain alphaMonFile.fa monomerOrder.txt significant_output.txt\n"
+  "   alphaChain alphaMonFile.txt monomerOrder.txt output.txt\n"
+  "Where alphaMonFile is a list of reads with alpha chains monomers parsed out, one read per\n"
+  "line, with the first word in the line being the read id and subsequent words the monomers\n"
+  "within the read. The monomerOrder.txt has one line per major monomer type with a word for\n"
+  "each variant. The lines are in the same order the monomers appear, with the last line\n"
+  "being followed in order by the first since they repeat.   The output.txt contains one line\n"
+  "for each monomer in the output, just containing the monomer symbol.\n"
   "options:\n"
   "   -size=N - Set max chain size, default %d\n"
   "   -fullOnly - Only output chains of size above\n"
   "   -chain=fileName - Write out word chain to file\n"
   "   -afterChain=fileName - Write out word chain after faux generation to file for debugging\n"
   "   -outSize=N - Output this many words.\n"
   "   -seed=N - Initialize random number with this seed for consistent results, otherwise\n"
   "             it will generate different results each time it's run.\n"
   , maxChainSize
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"size", OPTION_INT},