2ad067dae732bef5b7ab5ddc463fbaa68a33fca3
braney
  Wed Mar 20 15:42:23 2019 -0700
initialize htslib to use UDC

diff --git src/hg/utils/hubCheck/hubCheck.c src/hg/utils/hubCheck/hubCheck.c
index f7e4ce1..55470a0 100644
--- src/hg/utils/hubCheck/hubCheck.c
+++ src/hg/utils/hubCheck/hubCheck.c
@@ -6,30 +6,31 @@
 #include "bigWig.h"
 #include "bigBed.h"
 #include "dystring.h"
 #include "errCatch.h"
 #include "hgBam.h"
 #include "htmshell.h"
 #include "htmlPage.h"
 #include "hui.h"
 #include "net.h"
 #include "options.h"
 #include "trackDb.h"
 #include "trackHub.h"
 #include "udc.h"
 #include "vcf.h"
 #include "bedTabix.h"
+#include "knetUdc.h"
 
 #ifdef USE_HAL
 #include "halBlockViz.h"
 #endif
 
 static int cacheTime = 1;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hubCheck - Check a track data hub for integrity.\n"
   "usage:\n"
   "   hubCheck http://yourHost/yourDir/hub.txt\n"
   "options:\n"
@@ -735,30 +736,32 @@
 char *version = NULL;
 if (optionExists("version"))
     version = optionVal("version", NULL);
 checkOptions->version = version;
 
 char *extraFile = optionVal("extra", NULL);
 if (extraFile != NULL)
     addExtras(extraFile, checkOptions);
 
 cacheTime = optionInt("cacheTime", cacheTime);
 udcSetCacheTimeout(cacheTime);
 // UDC cache dir: first check for hg.conf setting, then override with command line option if given.
 setUdcCacheDir();
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 
+knetUdcInstall();  // make the htslib library use udc
+
 if (optionExists("settings"))
     {
     showSettings(checkOptions);
     return 0;
     }
 
 struct dyString *errors = newDyString(1024);
 if (trackHubCheck(argv[1], checkOptions, errors))
     {
     // uniquify and count errors
     struct slName *errs = slNameListFromString(errors->string, '\n');
     slUniqify(&errs, slNameCmp, slNameFree);
     int errCount = slCount(errs);
     printf("Found %d problem%s:\n", errCount, errCount == 1 ? "" : "s");
     printf("%s\n", slNameListToString(errs, '\n'));