Bits *bitsForIntersectingTable(struct sqlConnection *conn, struct region *region, int chromSize,
boolean isBpWise)
/* Get a bitmap that corresponds to the table we are intersecting with.
* Consult CGI vars to figure out what table it is. */
{
boolean invTable2 = cartCgiUsualBoolean(cart, hgtaInvertTable2, FALSE);
char *table2 = cartString(cart, hgtaIntersectTable);
struct hTableInfo *hti2 = getHti(database, table2, conn);
struct lm *lm2 = lmInit(64*1024);
Bits *bits2 = bitAlloc(chromSize+8);
struct bed *bedList2;
if (isBigWigTable(table2))
bedList2 = bigWigIntervalsToBed(conn, table2, region, lm2);
else
// We should go straight to raw beds here, not through the routines that
// do filter & intersections, because the secondary table has no filter
// and sure shouldn't be intersected. :)
bedList2 = getFilteredBeds(conn, table2, region, lm2, NULL);
if (!isBpWise)
expandZeroSize(bedList2, hti2->hasBlocks, chromSize);
bedOrBits(bits2, chromSize, bedList2, hti2->hasBlocks, 0);
if (invTable2)
bitNot(bits2, chromSize);
lmCleanup(&lm2);
return bits2;
}
static struct bed *bedTable2(struct sqlConnection *conn,
struct region *region, char *table2)
/* get a bed list, possibly complement, for table2 */
{
/* This use of bedTable rather than a bitmap is not really working. The
* rest of the table browser does intersection at the exon level, while
* the wig code, which this is part of, does it at the gene level. I
* noticed it while working on the corresponding routines for bigWig,
* which I'm building to work with bitmaps at the exon level. I'm not
* sure it's worth fixing this code since nobody has complained, and we're
* probably going to be doing mostly bigWig rather than wig in the future.
* -JK */
boolean invTable2 = cartCgiUsualBoolean(cart, hgtaInvertTable2, FALSE);
char *op = cartString(cart, hgtaIntersectOp);
struct bed *bedList = NULL;
struct lm *lm1 = lmInit(64*1024);
/* fetch table 2 as a bed list */
bedList = getFilteredBeds(conn, table2, region, lm1, NULL);
/* If table 2 bed list needs to be complemented (!table2), then do so */
if (invTable2 || sameString("none", op))
{
unsigned chromStart = 0; /* start == end == 0 */
unsigned chromEnd = 0; /* means do full chrom */
unsigned chromSize = hChromSize(database, region->chrom);
struct lm *lm2 = lmInit(64*1024);
struct bed *inverseBedList = NULL; /* new list */
if ((region->start != 0) || (region->end != 0))
{
chromStart = region->start;
chromEnd = region->end;
}
if ((struct bed *)NULL == bedList)
{
if (0 == region->end)
chromEnd = chromSize;
addBedElement(&inverseBedList, region->chrom, chromStart, chromEnd,
1, lm2);
}
else
inverseBedList=invertBedList(bedList, lm2, region->chrom, chromStart,
chromEnd, chromSize);
lmCleanup(&lm1); /* == bedFreeList(&bedList) */
return inverseBedList;
}
else
return bedList;
}
static struct bed *getIntersectedBeds(struct sqlConnection *conn,
char *table, struct region *region, struct lm *lm, int *retFieldCount)
/* Get list of beds in region that pass intersection
* (and filtering) */
{
struct bed *bedList = getFilteredBeds(conn, table, region, lm, retFieldCount);
/* wiggle tracks have already done the intersection if there was one */
if (!isWiggle(database, table) && anyIntersection())
{
struct bed *iBedList = intersectOnRegion(conn, region, table, bedList,
lm, retFieldCount);
return iBedList;
}
else
return bedList;
}
Bits *bitsForIntersectingTable(struct sqlConnection *conn, struct region *region, int chromSize,
boolean isBpWise)
/* Get a bitmap that corresponds to the table we are intersecting with.
* Consult CGI vars to figure out what table it is. */
{
boolean invTable2 = cartCgiUsualBoolean(cart, hgtaInvertTable2, FALSE);
char *table2 = cartString(cart, hgtaIntersectTable);
struct hTableInfo *hti2 = getHti(database, table2, conn);
struct lm *lm2 = lmInit(64*1024);
Bits *bits2 = bitAlloc(chromSize+8);
struct bed *bedList2 = getFilteredBeds(conn, table2, region, lm2, NULL);
if (!isBpWise)
expandZeroSize(bedList2, hti2->hasBlocks, chromSize);
bedOrBits(bits2, chromSize, bedList2, hti2->hasBlocks, 0);
if (invTable2)
bitNot(bits2, chromSize);
lmCleanup(&lm2);
return bits2;
}
