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/hg/pslPretty/pslPretty.c src/hg/pslPretty/pslPretty.c
index 994528e..076c551 100644
--- src/hg/pslPretty/pslPretty.c
+++ src/hg/pslPretty/pslPretty.c
@@ -4,45 +4,43 @@
 #include "hash.h"
 #include "options.h"
 #include "dystring.h"
 #include "dlist.h"
 #include "fa.h"
 #include "nib.h"
 #include "twoBit.h"
 #include "psl.h"
 #include "axt.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
-  "pslPretty - Convert PSL to human readable output\n"
+  "pslPretty - Convert PSL to human-readable output\n"
   "usage:\n"
   "   pslPretty in.psl target.lst query.lst pretty.out\n"
   "options:\n"
-  "   -axt - save in something like Scott Schwartz's axt format\n"
+  "   -axt             Save in format like Scott Schwartz's axt format.\n"
   "                    Note gaps in both sequences are still allowed in the\n"
-  "          output which not all axt readers will expect\n"
-  "   -dot=N Put out a dot every N records\n"
-  "   -long - Don't abbreviate long inserts\n"
-  "   -check=fileName - Output alignment checks to filename\n" 
-  "It's a really good idea if the psl file is sorted by target\n"
-  "if it contains multiple targets.  Otherwise this will be\n"
-  "very very slow.   The target and query lists can either be\n"
-  "fasta, 2bit or nib files, or a list of fasta, 2bit and/or nib files\n"
-  "one per line\n");
+  "                    output, which not all axt readers will expect.\n"
+  "   -dot=N           Output a dot every N records.\n"
+  "   -long            Don't abbreviate long inserts.\n"
+  "   -check=fileName  Output alignment checks to filename.\n" 
+  "It's recommended that the psl file be sorted by target if it contains\n"
+  "multiple targets; otherwise this will be extremely slow. The target and query\n"
+  "lists can be fasta, 2bit or nib files, or a list of these files, one per line.\n");
 }
 
 int dot = 0;
 boolean doShort = FALSE;
 struct axtScoreScheme *ss = NULL;
 
 struct seqFilePos
 /* Where a sequence is in a file. */
     {
     struct filePos *next;	/* Next in list. */
     char *name;	/* Sequence name. Allocated in hash. */
     char *file;	/* Sequence file name, allocated in hash. */
     long pos; /* Position in fa file/size of nib. */
     bool isNib;	/* True if a nib file. */
     bool isTwoBit;  /* True if a two bit file. */