c28c1ef92c57fb16bdb8b1ad6e78879d03d39311
donnak
  Mon Oct 14 13:47:24 2013 -0700
Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.
diff --git src/utils/nibFrag/nibFrag.c src/utils/nibFrag/nibFrag.c
index f842f54..9d2c034 100644
--- src/utils/nibFrag/nibFrag.c
+++ src/utils/nibFrag/nibFrag.c
@@ -12,33 +12,33 @@
     {"upper", OPTION_BOOLEAN},
     {"name", OPTION_STRING},
     {"dbHeader", OPTION_STRING},
     {"tbaHeader", OPTION_STRING},
     {NULL, 0}
 };
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "nibFrag - Extract part of a nib file as .fa (all bases/gaps lower case by default)\n"
   "usage:\n"
   "   nibFrag [options] file.nib start end strand out.fa\n"
   "where strand is + (plus) or m (minus)\n"
   "options:\n"
-  "   -masked - use lower case characters for bases meant to be masked out\n"
-  "   -hardMasked - use upper case for not masked-out and 'N' characters for masked-out bases\n"
-  "   -upper - use upper case characters for all bases\n"
+  "   -masked       Use lower-case characters for bases meant to be masked out\n"
+  "   -hardMasked   Use upper-case for not masked-out, and 'N' characters for masked-out bases\n"
+  "   -upper        Use upper-case characters for all bases\n"
   "   -name=name    Use given name after '>' in output sequence\n"
   "   -dbHeader=db  Add full database info to the header, with or without -name option\n"
   "   -tbaHeader=db Format header for compatibility with tba, takes database name as argument\n"
   );
 }
 
 void nibFrag(int options, char *nibFile, int start, int end, char strand, 
 	     char *faFile, int optUpper, boolean hardMask)
 /* nibFrag - Extract part of a nib file as .fa. */
 {
 struct dnaSeq *seq;
 char header[255];
 char name[128];
 int chromLength;