void doVcfTabixDetails(struct trackDb *tdb, char *item)
/* Show details of an alignment from a VCF file compressed and indexed by tabix. */
{
knetUdcInstall();
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
struct sqlConnection *conn = hAllocConnTrack(database, tdb);
char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, tdb->table, seqName);
hFreeConn(&conn);
doVcfDetailsCore(tdb, fileOrUrl, TRUE);
}
static void vcfTabixLoadItems(struct track *tg)
/* Load items in window from VCF file using its tabix index file. */
{
char *fileOrUrl = NULL;
/* Figure out url or file name. */
if (tg->parallelLoading)
{
/* do not use mysql during parallel-fetch load */
fileOrUrl = trackDbSetting(tg->tdb, "bigDataUrl");
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
fileOrUrl = bbiNameFromSettingOrTableChrom(tg->tdb, conn, tg->table, chromName);
hFreeConn(&conn);
}
if (isEmpty(fileOrUrl))
return;
int vcfMaxErr = -1;
struct vcfFile *vcff = NULL;
boolean hapClustEnabled = cartOrTdbBoolean(cart, tg->tdb, VCF_HAP_ENABLED_VAR, TRUE);
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
vcff = vcfTabixFileMayOpen(fileOrUrl, chromName, winStart, winEnd, vcfMaxErr, -1);
if (vcff != NULL)
{
filterRecords(vcff, tg->tdb);
if (hapClustEnabled && vcff->genotypeCount > 1 && vcff->genotypeCount < 3000 &&
(tg->visibility == tvPack || tg->visibility == tvSquish))
vcfHapClusterOverloadMethods(tg, vcff);
else
{
tg->items = vcfFileToPgSnp(vcff, tg->tdb);
// pgSnp bases coloring/display decision on count of items:
tg->customInt = slCount(tg->items);
}
// Don't vcfFileFree here -- we are using its string pointers!
}
}
errCatchEnd(errCatch);
if (errCatch->gotError || vcff == NULL)
{
if (isNotEmpty(errCatch->message->string))
tg->networkErrMsg = cloneString(errCatch->message->string);
tg->drawItems = bigDrawWarning;
tg->totalHeight = bigWarnTotalHeight;
}
errCatchFree(&errCatch);
}
void doVcfDetails(struct trackDb *tdb, char *item)
/* Show details of an alignment from an uncompressed VCF file. */
{
struct customTrack *ct = lookupCt(tdb->track);
struct sqlConnection *conn = NULL;
char *table = tdb->table;
if (ct)
{
conn = hAllocConn(CUSTOM_TRASH);
table = ct->dbTableName;
}
else
conn = hAllocConnTrack(database, tdb);
char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, table, seqName);
hFreeConn(&conn);
doVcfDetailsCore(tdb, fileOrUrl, FALSE);
}
static char *vcfFileName(struct trackDb *tdb, struct sqlConnection *conn, char *table, char *chrom)
// Look up the vcf or vcfTabix file name, using CUSTOM_TRASH if necessary.
{
boolean isCt = isCustomTrack(table);
char *dbTable = table;
struct sqlConnection *dbConn = conn;
if (isCt)
{
dbConn = hAllocConn(CUSTOM_TRASH);
struct customTrack *ct = ctLookupName(table);
dbTable = ct->dbTableName;
}
char *fileName = bbiNameFromSettingOrTableChrom(tdb, dbConn, dbTable, chrom);
if (isCt)
hFreeConn(&dbConn);
return fileName;
}
