4ac69dd9425c5437842f66d2034a8ba4867117fd
kent
  Fri Jul 7 12:25:52 2017 -0700
Making gfServer have a debugLog option.

diff --git src/gfServer/gfServer.c src/gfServer/gfServer.c
index 633e1f3..1976389 100644
--- src/gfServer/gfServer.c
+++ src/gfServer/gfServer.c
@@ -25,30 +25,31 @@
 
 static struct optionSpec optionSpecs[] = {
     {"canStop", OPTION_BOOLEAN},
     {"log", OPTION_STRING},
     {"logFacility", OPTION_STRING},
     {"mask", OPTION_BOOLEAN},
     {"maxAaSize", OPTION_INT},
     {"maxDnaHits", OPTION_INT},
     {"maxGap", OPTION_INT},
     {"maxNtSize", OPTION_INT},
     {"maxTransHits", OPTION_INT},
     {"minMatch", OPTION_INT},
     {"repMatch", OPTION_INT},
     {"seqLog", OPTION_BOOLEAN},
     {"ipLog", OPTION_BOOLEAN},
+    {"debugLog", OPTION_BOOLEAN},
     {"stepSize", OPTION_INT},
     {"tileSize", OPTION_INT},
     {"trans", OPTION_BOOLEAN},
     {"syslog", OPTION_BOOLEAN},
     {NULL, 0}
 };
 
 
 int maxNtSize = 40000;
 int maxAaSize = 8000;
 
 int minMatch = gfMinMatch;	/* Can be overridden from command line. */
 int tileSize = gfTileSize;	/* Can be overridden from command line. */
 int stepSize = 0;		/* Can be overridden from command line. */
 boolean doTrans = FALSE;	/* Do translation? */
@@ -89,30 +90,31 @@
   "   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"
   "                   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"
   "   -ipLog          Include user's IP in log file (not logged with -syslog).\n"
+  "   -debugLog       Include debugging info in log file.\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 (n-mer) 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, a quit message will actually take down the server.\n"
   ,	gfVersion, repMatch, maxDnaHits, maxTransHits, maxNtSize, maxAaSize
@@ -955,30 +957,32 @@
 minMatch = optionInt("minMatch", minMatch);
 maxDnaHits = optionInt("maxDnaHits", maxDnaHits);
 maxTransHits = optionInt("maxTransHits", maxTransHits);
 maxNtSize = optionInt("maxNtSize", maxNtSize);
 maxAaSize = optionInt("maxAaSize", maxAaSize);
 seqLog = optionExists("seqLog");
 ipLog = optionExists("ipLog");
 doMask = optionExists("mask");
 canStop = optionExists("canStop");
 if (argc < 2)
     usage();
 if (optionExists("log"))
     logOpenFile(argv[0], optionVal("log", NULL));
 if (optionExists("syslog"))
     logOpenSyslog(argv[0], optionVal("logFacility", NULL));
+if (optionExists("debugLog"))
+    logSetMinPriority("debug");
 
 if (sameWord(command, "direct"))
     {
     if (argc < 4)
         usage();
     genoFindDirect(argv[2], argc-3, argv+3);
     }
 else if (sameWord(command, "pcrDirect"))
     {
     if (argc < 5)
         usage();
     genoPcrDirect(argv[2], argv[3], argc-4, argv+4);
     }
 else if (sameWord(command, "start"))
     {