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/gfServer/gfServer.c src/gfServer/gfServer.c index 669d1c7..94efbe7 100644 --- src/gfServer/gfServer.c +++ src/gfServer/gfServer.c @@ -54,80 +54,79 @@ boolean doTrans = FALSE; /* Do translation? */ boolean allowOneMismatch = FALSE; int repMatch = 1024; /* Can be overridden from command line. */ 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" + "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 .nib or .2bit format files specified relative to the current directory.\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" + " To query a server with translated DNA sequence:\n" " gfServer transQuery host port probe.fa\n" - "To query server with PCR primers\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" + " To test PCR without starting server:\n" " gfServer pcrDirect fPrimer rPrimer file(s).nib\n" - "To figure out usage level\n" + " To figure out usage level:\n" " gfServer status host port\n" - "To get input file list\n" + " To get input file list:\n" " gfServer files host port\n" - "Options:\n" - " -tileSize=N size of n-mers to index. Default is 11 for nucleotides, 4 for\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 protiens.\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 protiens.\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" - " -ipLog Include user's IP in log file (not logged with -syslog)\n" - " -syslog Log to syslog\n" - " -logFacility=facility log to the specified syslog facility - default local0.\n" + " -log=logFile Keep a log file that records server requests.\n" + " -seqLog Include sequences in log file (not logged with -syslog).\n" + " -ipLog Include user's IP in log file (not logged with -syslog).\n" + " -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" + " -repMatch=N Number of occurrences of a tile (nmer) that triggers repeat masking the\n" + " tile. 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" + " -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 server.\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.