void addGaps(struct sqlConnection *conn, char *chrom, struct rbTree *rt)
/* Add gaps from gap table to range tree. */
{
struct sqlResult *sr = hExtendedChromQuery(conn, "gap", chrom, NULL, FALSE,
"chromStart,chromEnd", NULL);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
rangeTreeAdd(rt, sqlUnsigned(row[0]), sqlUnsigned(row[1]));
}
sqlFreeResult(&sr);
}
void tableCoverageIntoTree(struct hTableInfo *hti, struct trackDb *tdb, struct sqlConnection *conn,
char *chrom, int chromSize, struct rbTree *rt)
/* Find biggest gap in given chromosome in database table with chromosome coordinates */
{
char fields[512];
safef(fields, sizeof(fields), "%s,%s", hti->startField, hti->endField);
struct sqlResult *sr = hExtendedChromQuery(conn, hti->rootName, chrom, NULL, FALSE,
fields, NULL);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
rangeTreeAdd(rt, sqlUnsigned(row[0]), sqlUnsigned(row[1]));
}
sqlFreeResult(&sr);
}
static struct bed *getChromAsBed(
struct sqlConnection *conn,
char *db, char *table, /* Database and table. */
char *chrom,
struct lm *lm,
int *retFieldCount) /* Where to allocate memory. */
/* Return a bed list of all items in the given range in table.
* Cleanup result via lmCleanup(&lm) rather than bedFreeList. */
{
char *fields = NULL;
struct sqlResult *sr;
struct hTableInfo *hti;
struct bed *bedList=NULL, *bed;
char **row;
int fieldCount;
boolean isPsl, isGenePred, isBedWithBlocks;
boolean pslKnowIfProtein = FALSE, pslIsProtein = FALSE;
hti = hFindTableInfoDb(db, chrom, table);
if (hti == NULL)
errAbort("Could not find table info for table %s", table);
bedSqlFieldsExceptForChrom(hti, &fieldCount, &fields);
isPsl = htiIsPsl(hti);
isGenePred = sameString("exonEnds", hti->endsSizesField);
isBedWithBlocks = (
(sameString("chromStarts", hti->startsField) ||
sameString("blockStarts", hti->startsField))
&& sameString("blockSizes", hti->endsSizesField));
/* All beds have at least chrom,start,end. We omit the chrom
* from the query since we already know it. */
sr = hExtendedChromQuery(conn, table, chrom, NULL, FALSE, fields, NULL);
while (sr != NULL && (row = sqlNextRow(sr)) != NULL)
{
bed = bedFromRow(chrom, row, fieldCount, isPsl, isGenePred,
isBedWithBlocks, &pslKnowIfProtein, &pslIsProtein, lm);
slAddHead(&bedList, bed);
}
freez(&fields);
sqlFreeResult(&sr);
slReverse(&bedList);
*retFieldCount = fieldCount;
return(bedList);
}
