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 @@
" bigBed,\n"
" bedGraph,\n"
" GFF,\n"
" GTF,\n"
" WIG\n"
" bigWig,\n"
" BED detail,\n"
" Personal Genome SNP,\n"
" or PSL\n"
" formats. To configure the display, set\n"
" track\n"
" and"
" browser\n"
" line attributes as described in the \n"
" User's Guide.\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"
" BED,\n"
" bigBed,\n"
" bedGraph,\n"
" GFF,\n"
" GTF,\n"
" WIG,\n"
" bigWig,\n"
" MAF,\n"
" BAM,\n"
" BED detail,\n"
" Personal Genome SNP,\n"
+ " VCF,\n"
" or PSL\n"
" formats. To configure the display, set\n"
" track\n"
" and"
" browser\n"
" line attributes as described in the \n"
" User's Guide.\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"
" here.\n"
" Examples are\n"
" here.\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)