989c9aeaab7cb44cf18de57003b0044e229b6f28
donnak
  Mon Oct 14 11:39:29 2013 -0700
Fixed some typos and formatting probs in conjunction with updating blat spec.
diff --git src/gfClient/gfClient.c src/gfClient/gfClient.c
index bdb55d0..b1e90ea 100644
--- src/gfClient/gfClient.c
+++ src/gfClient/gfClient.c
@@ -28,66 +28,66 @@
 int minScore = 30;
 double minIdentity = 90;
 char *outputFormat = "psl";
 char *qType = "dna";
 char *tType = "dna";
 
 void usage()
 /* Explain usage and exit. */
 {
 printf(
   "gfClient v. %s - A client for the genomic finding program that produces a .psl file\n"
   "usage:\n"
   "   gfClient host port seqDir in.fa out.psl\n"
   "where\n"
   "   host is the name of the machine running the gfServer\n"
-  "   port is the same as you started the gfServer with\n"
+  "   port is the same port that you started the gfServer with\n"
   "   seqDir is the path of the .nib or .2bit files relative to the current dir\n"
   "       (note these are needed by the client as well as the server)\n"
   "   in.fa is a fasta format file.  May contain multiple records\n"
-  "   out.psl where to put the output\n"
+  "   out.psl is where to put the output\n"
   "options:\n"
   "   -t=type     Database type.  Type is one of:\n"
   "                 dna - DNA sequence\n"
   "                 prot - protein sequence\n"
   "                 dnax - DNA sequence translated in six frames to protein\n"
-  "               The default is dna\n"
+  "               The default is dna.\n"
   "   -q=type     Query type.  Type is one of:\n"
   "                 dna - DNA sequence\n"
   "                 rna - RNA sequence\n"
   "                 prot - protein sequence\n"
   "                 dnax - DNA sequence translated in six frames to protein\n"
   "                 rnax - DNA sequence translated in three frames to protein\n"
-  "   -prot       Synonymous with -d=prot -q=prot\n"
-  "   -dots=N   Output a dot every N query sequences\n"
-  "   -nohead   Suppresses psl five line header\n"
-  "   -minScore=N sets minimum score.  This is twice the matches minus the \n"
-  "               mismatches minus some sort of gap penalty.  Default is 30\n"
+  "   -prot       Synonymous with -d=prot -q=prot.\n"
+  "   -dots=N     Output a dot every N query sequences.\n"
+  "   -nohead     Suppresses 5-line psl header.\n"
+  "   -minScore=N Sets minimum score.  This is twice the matches minus the \n"
+  "               mismatches minus some sort of gap penalty.  Default is 30.\n"
   "   -minIdentity=N Sets minimum sequence identity (in percent).  Default is\n"
   "               90 for nucleotide searches, 25 for protein or translated\n"
   "               protein searches.\n"
   "   -out=type   Controls output file format.  Type is one of:\n"
-  "                   psl - Default.  Tab separated format without actual sequence\n"
-  "                   pslx - Tab separated format with sequence\n"
+  "                 psl - Default.  Tab-separated format without actual sequence\n"
+  "                 pslx - Tab-separated format with sequence\n"
   "                 axt - blastz-associated axt format\n"
   "                 maf - multiz-associated maf format\n"
   "                 sim4 - similar to sim4 format\n"
   "                 wublast - similar to wublast format\n"
   "                 blast - similar to NCBI blast format\n"
   "                 blast8- NCBI blast tabular format\n"
   "                 blast9 - NCBI blast tabular format with comments\n"
-  "   -maxIntron=N  Sets maximum intron size. Default is %d\n",
+  "   -maxIntron=N Sets maximum intron size. Default is %d.\n",
                         gfVersion, ffIntronMaxDefault);
 exit(-1);
 }
 
 
 struct gfOutput *gvo;
 
 void gfClient(char *hostName, char *portName, char *tSeqDir, char *inName, 
 	char *outName, char *tTypeName, char *qTypeName)
 /* gfClient - A client for the genomic finding program that produces a .psl file. */
 {
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 static bioSeq seq;
 FILE *out = mustOpen(outName, "w");
 enum gfType qType = gfTypeFromName(qTypeName);