766230b7caec3cf15b9ec616b6fe329bbbfe00ca
galt
  Mon Jan 28 17:08:07 2013 -0800
Jim shortens it.
diff --git src/gfServer/gfServer.c src/gfServer/gfServer.c
index 6a8b4b6..669d1c7 100644
--- src/gfServer/gfServer.c
+++ src/gfServer/gfServer.c
@@ -57,31 +57,31 @@
 int maxDnaHits = 100;   /* Can be overridden from command line. */
 int maxTransHits = 200; /* Can be overridden from command line. */
 int maxGap = gfMaxGap;
 boolean seqLog = FALSE;
 boolean ipLog = FALSE;
 boolean doMask = FALSE;
 boolean canStop = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "gfServer v %s - Make a server to quickly find where DNA occurs in genome.\n"
   "To set up a server:\n"
   "   gfServer start host port file(s)\n"
-  "   Where the files are in .nib or .2bit format\n"
+  "   Where the files are .nib or .2bit format files specified relative to the current directory.\n"
   "To remove a server:\n"
   "   gfServer stop host port\n"
   "To query a server with DNA sequence:\n"
   "   gfServer query host port probe.fa\n"
   "To query a server with protein sequence:\n"
   "   gfServer protQuery host port probe.fa\n"
   "To query a server with translated dna sequence:\n"
   "   gfServer transQuery host port probe.fa\n"
   "To query server with PCR primers\n"
   "   gfServer pcr host port fPrimer rPrimer maxDistance\n"
   "To process one probe fa file against a .nib format genome (not starting server):\n"
   "   gfServer direct probe.fa file(s).nib\n"
   "To test pcr without starting server:\n"
   "   gfServer pcrDirect fPrimer rPrimer file(s).nib\n"
   "To figure out usage level\n"
@@ -104,45 +104,47 @@
   "   -syslog    Log to syslog\n"
   "   -logFacility=facility log to the specified syslog facility - default local0.\n"
   "   -mask      Use masking from nib file.\n"
   "   -repMatch=N Number of occurrences of a tile (nmer) that trigger repeat masking the tile.\n"
   "               Default is %d.\n"
   "   -maxDnaHits=N Maximum number of hits for a dna query that are sent from the server.\n"
   "               Default is %d.\n"
   "   -maxTransHits=N Maximum number of hits for a translated query that are sent from the server.\n"
   "               Default is %d.\n"
   "   -maxNtSize=N Maximum size of untranslated DNA query sequence\n"
   "               Default is %d\n"
   "   -maxAaSize=N Maximum size of protein or translated DNA queries\n"
   "               Default is %d\n"
   "   -canStop If set then a quit message will actually take down the\n"
   "            server\n"
-  "Note about file(s) specified in the start command:\n"
-  "    The path(s) specified here are sent back exactly as-is\n"
-  "    to clients such as gfClient, hgBlat, webBlat.\n"
-  "    It is intended that relative paths are used.\n"
-  "    Absolute paths starting with '/' tend not to work\n"
-  "    unless the client is on the same machine as the server.\n"
-  "    For use with hgBlat and webBlat, cd to the directory where the file is\n"
-  "    and use the plain file name with no slashes.\n"
-  "      hgBlat will append the path(s) given to dbDb.nibPath.\n"
-  "     webBlat will append the path(s) given to path specified in webBlat.cfg.\n"
-  "    gfClient will append the path(s) given to the seqDir path specified.\n"
   ,	gfVersion, repMatch, maxDnaHits, maxTransHits, maxNtSize, maxAaSize
   );
 
 }
+/*
+  Note about file(s) specified in the start command:
+      The path(s) specified here are sent back exactly as-is
+      to clients such as gfClient, hgBlat, webBlat.
+      It is intended that relative paths are used.
+      Absolute paths starting with '/' tend not to work
+      unless the client is on the same machine as the server.
+      For use with hgBlat and webBlat, cd to the directory where the file is
+      and use the plain file name with no slashes.
+        hgBlat will append the path(s) given to dbDb.nibPath.
+       webBlat will append the path(s) given to path specified in webBlat.cfg.
+      gfClient will append the path(s) given to the seqDir path specified.
+*/
 
 void genoFindDirect(char *probeName, int fileCount, char *seqFiles[])
 /* Don't set up server - just directly look for matches. */
 {
 struct genoFind *gf = NULL;
 struct lineFile *lf = lineFileOpen(probeName, TRUE);
 struct dnaSeq seq;
 int hitCount = 0, clumpCount = 0, oneHit;
 ZeroVar(&seq);
 
 if (doTrans)
     errAbort("Don't support translated direct stuff currently, sorry");
 
 gf = gfIndexNibsAndTwoBits(fileCount, seqFiles, minMatch, maxGap, 
 	tileSize, repMatch, FALSE,