static void wikiTrackFilteredBedOnRegion(
struct region *region, /* Region to get data from. */
struct hash *idHash, /* Hash of identifiers or NULL */
struct bedFilter *bf, /* Filter or NULL */
struct lm *lm, /* Local memory pool. */
struct bed **pBedList /* Output get's appended to this list */
)
/* Get the wikiTrack items passing filter on a single region. */
{
struct bed *bed;
int fieldCount = 6;
char query[512];
int rowOffset;
char **row;
struct sqlConnection *wikiConn = wikiConnect();
struct sqlResult *sr = NULL;
char where[512];
char *filter = filterClause(wikiDbName(), WIKI_TRACK_TABLE, region->chrom, NULL);
if (filter)
sqlSafefFrag(where, sizeof(where), "db='%s' AND %-s", database, filter);
else
sqlSafefFrag(where, sizeof(where), "db='%s'", database);
sqlSafef(query, sizeof(query), "select * from %s", WIKI_TRACK_TABLE);
sr = hRangeQuery(wikiConn, WIKI_TRACK_TABLE, region->chrom,
region->start, region->end, where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, fieldCount);
if ((idHash == NULL || hashLookup(idHash, bed->name)) &&
(bf == NULL || bedFilterOne(bf, bed)))
{
struct bed *copy = lmCloneBed(bed, lm);
slAddHead(pBedList, copy);
}
}
sqlFreeResult(&sr);
wikiDisconnect(&wikiConn);
}
static void addFilteredBedsOnRegion(struct bbiFile *bbi, struct region *region,
char *table, struct asFilter *filter, struct lm *bedLm, struct bed **pBedList)
/* Add relevant beds in reverse order to pBedList */
{
struct lm *bbLm = lmInit(0);
struct bigBedInterval *ivList = NULL, *iv;
ivList = bigBedIntervalQuery(bbi, region->chrom, region->start, region->end, 0, bbLm);
char *row[bbi->fieldCount];
char startBuf[16], endBuf[16];
for (iv = ivList; iv != NULL; iv = iv->next)
{
bigBedIntervalToRow(iv, region->chrom, startBuf, endBuf, row, bbi->fieldCount);
if (asFilterOnRow(filter, row))
{
struct bed *bed = bedLoadN(row, bbi->definedFieldCount);
struct bed *lmBed = lmCloneBed(bed, bedLm);
slAddHead(pBedList, lmBed);
bedFree(&bed);
}
}
lmCleanup(&bbLm);
}
struct bed *getWiggleAsBed(
char *db, char *table, /* Database and table. */
struct region *region, /* Region to get data for. */
char *filter, /* Filter to add to SQL where clause if any. */
struct hash *idHash, /* Restrict to id's in this hash if non-NULL. */
struct lm *lm, /* Where to allocate memory. */
struct sqlConnection *conn) /* SQL connection to work with */
/* Return a bed list of all items in the given range in table.
* Cleanup result via lmCleanup(&lm) rather than bedFreeList. */
/* filter, idHash and lm are currently unused, perhaps future use */
{
struct bed *bedList=NULL;
char splitTableOrFileName[HDB_MAX_TABLE_STRING];
struct customTrack *ct = NULL;
boolean isCustom = FALSE;
boolean hasConstraint = FALSE;
struct wiggleDataStream *wds = NULL;
unsigned long long valuesMatched = 0;
int operations = wigFetchBed;
char *dataConstraint;
double ll = 0.0;
double ul = 0.0;
char *table2 = NULL;
struct bed *intersectBedList = NULL;
int maxOut;
WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */
if (hasConstraint)
freeMem(dataConstraint); /* been cloned into wds */
maxOut = bigFileMaxOutput();
wds->setMaxOutput(wds, maxOut);
wds->setChromConstraint(wds, region->chrom);
wds->setPositionConstraint(wds, region->start, region->end);
if (table2)
intersectBedList = bedTable2(conn, region, table2);
if (isCustom)
{
if (ct->dbTrack)
{
unsigned span = 0;
struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH);
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
valuesMatched = getWigglePossibleIntersection(wds, region,
CUSTOM_TRASH, table2, &intersectBedList,
splitTableOrFileName, operations);
span = minSpan(trashConn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
hFreeConn(&trashConn);
}
else
valuesMatched = getWigglePossibleIntersection(wds, region, NULL, table2,
&intersectBedList, splitTableOrFileName, operations);
}
else
{
if (conn == NULL)
errAbort( "getWiggleAsBed: NULL conn given for database table");
if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL))
{
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
unsigned span = 0;
/* XXX TBD, watch for a span limit coming in as an SQL filter */
span = minSpan(conn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region, database,
table2, &intersectBedList, splitTableOrFileName, operations);
}
}
if (valuesMatched > 0)
{
struct bed *bed;
wds->sortResults(wds);
for (bed = wds->bed; bed != NULL; bed = bed->next)
{
struct bed *copy = lmCloneBed(bed, lm);
slAddHead(&bedList, copy);
}
slReverse(&bedList);
}
wiggleDataStreamFree(&wds);
return bedList;
} /* struct bed *getWiggleAsBed() */
