gfServer - Make a server to quickly find where DNA occurs in genome.
To set up a server:
   gfServer start host port file(s).nib
To remove a server:
   gfServer stop host port
To query a server with DNA sequence:
   gfServer query host port probe.fa
To query a server with protein sequence:
   gfServer protQuery host port probe.fa
To query a server with translated dna sequence:
   gfServer transQuery host port probe.fa
To process one probe fa file against a .nib format genome (not starting server):
   gfServer direct probe.fa file(s).nib
To figure out usage level
   gfServer status host port
To get input file list
   gfServer files host port
Options:
   -tileSize=N size of n-mers to index.  Default is 11 for nucleotides, 4 for
               proteins (or translated nucleotides).
   -minMatch=N Number of n-mer matches that trigger detailed alignment
               Default is 2 for nucleotides, 3 for protiens.
   -maxGap=N   Number of insertions or deletions allowed between n-mers.
               Default is 2 for nucleotides, 0 for protiens.
   -trans  Translate database to protein in 6 frames.  Note: it is best
           to run this on RepeatMasked data in this case.
   -log=logFile keep a log file that records server requests.
   -seqLog    Include sequences in log file