84dba0006acf65324bb843abee1e11ad02c0a912
markd
  Sun Jul 5 20:01:10 2020 -0700
some cleanup about hgBlat

diff --git src/gfServer/gfServer.c src/gfServer/gfServer.c
index 9c2c43f..7c8a626 100644
--- src/gfServer/gfServer.c
+++ src/gfServer/gfServer.c
@@ -601,36 +601,36 @@
 loctime = localtime (&curtime);  /* Convert it to local time representation. */
 strftime (timestr, sizeof(timestr), "%Y-%m-%d %H:%M", loctime); /* formate datetime as string */
 								
 logInfo("gfServer version %s on host %s, port %s  (%s)", gfVersion, 
 	hostName, portName, timestr);
 struct hash *perSeqMaxHash = maybePerSeqMax(fileCount, seqFiles);
 
 time_t startIndexTime = clock1000();
 if (indexFile == NULL)
     {
     char *desc = doTrans ? "translated" : "untranslated";
     uglyf("starting %s server...\n", desc);
     logInfo("setting up %s index", desc);
     gfIdx = genoFindIndexBuild(fileCount, seqFiles, minMatch, maxGap, tileSize, repMatch, doTrans, NULL,
                                allowOneMismatch, doMask, stepSize, noSimpRepMask);
-    logInfo("indexing building complete in  %4.3f seconds", 0.001 * (clock1000() - startIndexTime));
+    logInfo("index building completed in %4.3f seconds", 0.001 * (clock1000() - startIndexTime));
     }
 else
     {
     gfIdx = genoFindIndexLoad(indexFile, doTrans);
-    logInfo("indexing loading complete in  %4.3f seconds", 0.001 * (clock1000() - startIndexTime));
+    logInfo("index loading completed in %4.3f seconds", 0.001 * (clock1000() - startIndexTime));
     }
 
 /* Set up socket.  Get ready to listen to it. */
 socketHandle = netAcceptingSocket(port, 100);
 if (socketHandle < 0)
     errAbort("Fatal Error: Unable to open listening socket on port %d.", port);
 
 logInfo("Server ready for queries!");
 printf("Server ready for queries!\n");
 int connectFailCount = 0;
 for (;;)
     {
     ZeroVar(&fromAddr);
     fromLen = sizeof(fromAddr);
     connectionHandle = accept(socketHandle, (struct sockaddr*)&fromAddr, &fromLen);
@@ -1166,41 +1166,46 @@
 netSendString(STDOUT_FILENO, buf);
 netSendString(STDOUT_FILENO, "end");
 }
 
 static void dynamicServer(char* rootDir)
 /* dynamic server for inetd. Read query from stdin, open index, query, respond, exit.
  * only one query at a time */
 {
 // make sure error is logged
 pushWarnHandler(dynWarnErrorVa);
 
 char *command, *genomeName;
 int qSize;
 boolean isTrans;
 dynReadCommand(&command, &qSize, &isTrans, &genomeName);
+logInfo("dynserver: %s %s %s size=%d ", command, genomeName, (isTrans ? "trans" : "untrans"), qSize);
 
+time_t startTime = clock1000();
 char seqFile[PATH_LEN];
 char *seqFiles[1] = {seqFile};  // functions expect list of files
 char gfIdxFile[PATH_LEN];
 dynGetDataFiles(rootDir, genomeName, isTrans, seqFiles[0], gfIdxFile);
+logInfo("dynserver: index loading completed in %4.3f seconds", 0.001 * (clock1000() - startTime));
+startTime = clock1000();
 
 struct genoFindIndex *gfIdx = genoFindIndexLoad(gfIdxFile, isTrans);
 if (endsWith(command, "Info"))
     dynamicServerInfo(command, genomeName, gfIdx);
 else
     dynamicServerQuery(command, qSize, genomeName, seqFiles, gfIdx);
+logInfo("dynserver: %s completed in %4.3f seconds", command, 0.001 * (clock1000() - startTime));
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 char *command;
 
 gfCatchPipes();
 dnaUtilOpen();
 optionInit(&argc, argv, optionSpecs);
 command = argv[1];
 if (optionExists("trans"))
     {
     doTrans = TRUE;
     tileSize = 4;