e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/utils/faToNib/faToNib.c src/utils/faToNib/faToNib.c
index 7220f6b..605a572 100644
--- src/utils/faToNib/faToNib.c
+++ src/utils/faToNib/faToNib.c
@@ -1,58 +1,61 @@
 /* faToNib - Convert from .fa to .nib format. */
+
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "options.h"
 #include "nib.h"
 #include "fa.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faToNib - Convert from .fa to .nib format\n"
   "usage:\n"
   "   faToNib [options] in.fa out.nib\n"
   "options:\n"
   "   -softMask  Create nib that soft-masks lower-case sequence.\n"
   "   -hardMask  Create nib that hard-masks lower-case sequence.\n");
 }
 
 void maskLower(struct dnaSeq *seq)
 /* Convert upper case to lower case and lower case to 'n' */
 {
 DNA *dna = seq->dna, base;
 int i, size = seq->size;
 for (i=0; i<size; ++i)
     {
     base = dna[i];
     if (isupper(base))
 	base = tolower(base);
     else
         base = 'n';
     dna[i] = base;
     }
 }
 
 void faToNib(int options, char *in, char *out)
 /* faToNib - Convert from .fa to .nib format. */
 {
 struct dnaSeq *seq = faReadAllMixed(in);
 if (slCount(seq) > 1)
     errAbort("faToNib only works on fa files containing a single sequence.");
 if (optionExists("hardMask"))
     maskLower(seq);
 nibWriteMasked(options, seq, out);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 int options = 0;
 optionHash(&argc, argv);
 if (optionExists("softMask"))
     options = NIB_MASK_MIXED;
 if (argc != 3)
     usage();
 faToNib(options, argv[1], argv[2]);
 return 0;
 }