void indexedChainSubsetOnT(struct indexedChain *ixc, int subStart, int subEnd,
struct chain **retSubChain, struct chain **retChainToFree)
/* Extract subset of chain that has been indexed. */
{
struct range *r = rangeTreeAllOverlapping(ixc->blockTree, subStart, subEnd);
if (r == NULL)
*retSubChain = *retChainToFree = NULL;
else
chainFastSubsetOnT(ixc->chain, r->val, subStart, subEnd, retSubChain, retChainToFree);
}
void chainSubsetOnT(struct chain *chain, int subStart, int subEnd,
struct chain **retSubChain, struct chain **retChainToFree)
/* Get subchain of chain bounded by subStart-subEnd on
* target side. Return result in *retSubChain. In some
* cases this may be the original chain, in which case
* *retChainToFree is NULL. When done call chainFree on
* *retChainToFree. The score and id fields are not really
* properly filled in. */
{
/* Find first relevant block. */
struct cBlock *firstBlock;
for (firstBlock = chain->blockList; firstBlock != NULL; firstBlock = firstBlock->next)
{
if (firstBlock->tEnd > subStart)
break;
}
chainFastSubsetOnT(chain, firstBlock, subStart, subEnd, retSubChain, retChainToFree);
}