struct rbTree *bedBkToTree(struct binKeeper *bk)
/* Make a rangeTree covering all exons in tree. */
{
struct binElement *el, *list = binKeeperFindAll(bk);
struct rbTree *tree = rangeTreeNew();
for (el = list; el != NULL; el = el->next)
{
struct bed *bed = el->val;
bedIntoRangeTree(bed, tree);
}
slFreeList(&list);
return tree;
}
void doStrand(struct bed *start, struct bed *end, FILE *f)
/* Assuming all beds from start up to end are on same strand,
* make a merged bed with all their blocks and output it. */
{
struct rbTree *rangeTree = rangeTreeNew();
struct bed *bed;
for (bed = start; bed != end; bed = bed->next)
bedIntoRangeTree(bed, rangeTree);
bed = bedFromRangeTree(rangeTree, start->chrom, start->name, start->strand);
bedTabOutN(bed, 12, f);
bedFree(&bed);
rangeTreeFree(&rangeTree);
}
void geneAddBed(struct gene *gene, struct bed *bed)
/* Add a bed into gene. */
{
slAddHead(&gene->txList, bed);
bedIntoRangeTree(bed, gene->exonTree);
}
