3c5f6de8a9739eb8ddaf1cb233460e0bba9e5321
markd
  Fri Dec 11 21:32:23 2020 -0800
fixed documention issues

diff --git src/gfServer/gfServer.c src/gfServer/gfServer.c
index 8d6f87e..f5afe9a 100644
--- src/gfServer/gfServer.c
+++ src/gfServer/gfServer.c
@@ -108,32 +108,34 @@
   "     with a persistent server as with 'start -indexFile or a dynamic server.\n"
   "     They must follow the naming convention for for dynamic servers.\n"
   "   To run a dynamic server (usually called by xinetd):\n"
   "      gfServer dynserver rootdir\n"
   "     Data files for genomes are found relative to the root directory.\n"
   "     Queries are made using the prefix of the file path relative to the root\n"
   "     directory.  The files $genome.2bit, $genome.untrans.gfidx, and\n"
   "     $genome.trans.gfidx are required. Typically the structure will be in\n"
   "     the form:\n"
   "         $rootdir/$genomeDataDir/$genome.2bit\n"
   "         $rootdir/$genomeDataDir/$genome.untrans.gfidx\n"
   "         $rootdir/$genomeDataDir/$genome.trans.gfidx\n"
   "     in this case, one would call gfClient with \n"
   "         -genome=$genome -genomeDataDir=$genomeDataDir\n"
   "     Often $genomeDataDir will be the same name as $genome, however it\n"
-  "     can be a multi-level path.  The $genomeDataDir may also be an absolute\n"
-  "     path.\n"
+  "     can be a multi-level path. For instance:\n"
+  "          GCA/902/686/455/GCA_902686455.1_mSciVul1.1/\n"
+  "     The translated or untranslated index maybe omitted if there is no\n"
+  "     need to handle that type of request.\n"
   "     The -perSeqMax functionality can be implemented by creating a file\n"
   "         $rootdir/$genomeDataDir/$genome.perseqmax\n"
   "\n"
   "options:\n"
   "   -tileSize=N     Size of n-mers to index.  Default is 11 for nucleotides, 4 for\n"
   "                   proteins (or translated nucleotides).\n"
   "   -stepSize=N     Spacing between tiles. Default is tileSize.\n"
   "   -minMatch=N     Number of n-mer matches that trigger detailed alignment.\n"
   "                   Default is 2 for nucleotides, 3 for proteins.\n"
   "   -maxGap=N       Number of insertions or deletions allowed between n-mers.\n"
   "                   Default is 2 for nucleotides, 0 for proteins.\n"
   "   -trans          Translate database to protein in 6 frames.  Note: it is best\n"
   "                   to run this on RepeatMasked data in this case.\n"
   "   -log=logFile    Keep a log file that records server requests.\n"
   "   -seqLog         Include sequences in log file (not logged with -syslog).\n"