1dd2ddbe9355485bb194198cb94e89e860acf7de
angie
  Fri Sep 30 10:10:20 2011 -0700
Feature #986 (VCF+tabix): mention VCF in hgCustom's list of supported formats.
diff --git src/hg/hgCustom/hgCustom.c src/hg/hgCustom/hgCustom.c
index 1977ba9..c4a40c5 100644
--- src/hg/hgCustom/hgCustom.c
+++ src/hg/hgCustom/hgCustom.c
@@ -101,48 +101,49 @@
   " <A TARGET=_BLANK HREF='../goldenPath/help/bigBed.html'>bigBed</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/bedgraph.html'>bedGraph</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#GFF'>GFF</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#GTF'>GTF</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/wiggle.html'>WIG</A>\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/bigWig.html'>bigWig</A>,\n"
   " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format1.7'>BED detail</A>,\n"
   " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format10'>Personal Genome SNP</A>,\n"
   " or <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#PSL'>PSL</A>\n"
   " formats. To configure the display, set\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#TRACK'>track</A>\n"
   " and"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#BROWSER'>browser</A>\n"
   " line attributes as described in the \n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html'>User's Guide</A>.\n"
-  " URLs for data in the bigBed, bigWig and BAM formats must be embedded in a track\n"
+  " URLs for data in the bigBed, bigWig BAM and VCF formats must be embedded in a track\n"
   " line in the box below.\n"
   );
   }
 else
   {
   puts(" Data must be formatted in\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#BED'>BED</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/bigBed.html'>bigBed</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/bedgraph.html'>bedGraph</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#GFF'>GFF</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#GTF'>GTF</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/wiggle.html'>WIG</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/bigWig.html'>bigWig</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/maf.html'>MAF</A>,\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/bam.html'>BAM</A>,\n"
   " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format1.7'>BED detail</A>,\n"
   " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format10'>Personal Genome SNP,</A>\n"
+  " <A TARGET=_BLANK HREF='../goldenPath/help/vcf.html'>VCF</A>,\n"
   " or <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#PSL'>PSL</A>\n"
   " formats. To configure the display, set\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#TRACK'>track</A>\n"
   " and"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#BROWSER'>browser</A>\n"
   " line attributes as described in the \n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html'>User's Guide</A>.\n"
   " URLs for data in the bigBed and bigWig formats must be embedded in a track\n"
   " line in the box below.\n"
   " Publicly available custom tracks are listed\n"
   " <A HREF='../goldenPath/customTracks/custTracks.html'>here</A>.\n"
   " Examples are\n"
   " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#EXAMPLE1'>here</A>.\n"
   );
   }
@@ -1042,35 +1043,35 @@
 char *selectedTable = NULL;
 struct customTrack *ct = NULL;
 boolean ctUpdated = FALSE;
 char *initialDb = NULL;
 
 long thisTime = clock1000();
 
 cart = theCart;
 measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
 initialDb = cloneString(cartString(cart, "db"));
 getDbAndGenome(cart, &database, &organism, oldVars);
 
 setUdcCacheDir();
 customFactoryEnableExtraChecking(TRUE);
 
-#if (defined USE_BAM && defined KNETFILE_HOOKS)
+#if ((defined USE_BAM || defined USE_TABIX) && defined KNETFILE_HOOKS)
 knetUdcInstall();
 if (udcCacheTimeout() < 300)
     udcSetCacheTimeout(300);
-#endif//def USE_BAM && KNETFILE_HOOKS
+#endif//def (USE_BAM || USE_TABIX) && KNETFILE_HOOKS
 
 if (sameString(initialDb, "0"))
     {
     /* when an organism is selected from the custom track management page,
      * set the database to be the default only if it has custom tracks.
      * Otherwise, pick an assembly for that organism that does have custom tracks. */
     struct dbDb *dbDb, *dbDbs = getCustomTrackDatabases();
     char *dbWithCts = NULL;
     for (dbDb = dbDbs; dbDb != NULL; dbDb = dbDb->next)
         {
         if (sameString(database, dbDb->name))
             break;
         if (sameString(organism, dbDb->organism))
             {
             if (!dbWithCts)