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/twoBitToFa/twoBitToFa.c src/utils/twoBitToFa/twoBitToFa.c
index 717cb51..bdfd119 100644
--- src/utils/twoBitToFa/twoBitToFa.c
+++ src/utils/twoBitToFa/twoBitToFa.c
@@ -7,41 +7,41 @@
 #include "fa.h"
 #include "twoBit.h"
 #include "bPlusTree.h"
 #include "basicBed.h"
 #include "udc.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "twoBitToFa - Convert all or part of .2bit file to fasta\n"
   "usage:\n"
   "   twoBitToFa input.2bit output.fa\n"
   "options:\n"
-  "   -seq=name - restrict this to just one sequence\n"
-  "   -start=X  - start at given position in sequence (zero-based)\n"
-  "   -end=X - end at given position in sequence (non-inclusive)\n"
-  "   -seqList=file - file containing list of the desired sequence names \n"
+  "   -seq=name       Restrict this to just one sequence.\n"
+  "   -start=X        Start at given position in sequence (zero-based).\n"
+  "   -end=X          End at given position in sequence (non-inclusive).\n"
+  "   -seqList=file   File containing list of the desired sequence names \n"
   "                   in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189\n"
-  "                    where coordinates are half-open zero-based, i.e. [start,end)\n"
-  "   -noMask - convert sequence to all upper case\n"
-  "   -bpt=index.bpt - use bpt index instead of built in one\n"
-  "   -bed=input.bed - grab sequences specified by input.bed. Will exclude introns\n"
-  "   -bedPos        - with -bed, to use chrom:start-end as the fasta ID in output.fa\n"
-  "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
+  "                   where coordinates are half-open zero-based, i.e. [start,end).\n"
+  "   -noMask         Convert sequence to all upper case.\n"
+  "   -bpt=index.bpt  Use bpt index instead of built-in one.\n"
+  "   -bed=input.bed  Grab sequences specified by input.bed. Will exclude introns.\n"
+  "   -bedPos         With -bed, use chrom:start-end as the fasta ID in output.fa.\n"
+  "   -udcDir=/dir/to/cache  Place to put cache for remote bigBed/bigWigs.\n"
   "\n"
   "Sequence and range may also be specified as part of the input\n"
   "file name using the syntax:\n"
   "      /path/input.2bit:name\n"
   "   or\n"
   "      /path/input.2bit:name\n"
   "   or\n"
   "      /path/input.2bit:name:start-end\n"
   );
 }
 
 char *clSeq = NULL;	/* Command line sequence. */
 int clStart = 0;	/* Start from command line. */
 int clEnd = 0;		/* End from command line. */
 char *clSeqList = NULL; /* file containing list of seq names */