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 oneChromInput(char *database, char *chrom, int chromSize,
char *rangeTrack, char *expTrack,
struct hash *refLinkHash, struct hash *erHash, FILE *f)
/* Read in info for one chromosome. */
{
struct binKeeper *rangeBk = binKeeperNew(0, chromSize);
struct binKeeper *expBk = binKeeperNew(0, chromSize);
struct binKeeper *knownBk = binKeeperNew(0, chromSize);
struct bed *rangeList = NULL, *range;
struct bed *expList = NULL;
struct genePred *knownList = NULL;
struct rangeInfo *riList = NULL, *ri;
struct hash *riHash = hashNew(0); /* rangeInfo values. */
struct binElement *rangeBeList = NULL, *rangeBe, *beList = NULL, *be;
/* Load up data from database. */
rangeList = loadBed(database, chrom, rangeTrack, 12, rangeBk);
expList = loadBed(database, chrom, expTrack, 15, expBk);
knownList = loadGenePred(database, chrom, "refGene", knownBk);
/* Build range info basics. */
rangeBeList = binKeeperFindAll(rangeBk);
for (rangeBe = rangeBeList; rangeBe != NULL; rangeBe = rangeBe->next)
{
range = rangeBe->val;
AllocVar(ri);
slAddHead(&riList, ri);
hashAddSaveName(riHash, range->name, ri, &ri->id);
ri->range = range;
ri->commonName = findCommonName(range, knownBk, refLinkHash);
}
slReverse(&riList);
/* Mark split ones. */
beList = binKeeperFindAll(expBk);
for (be = beList; be != NULL; be = be->next)
{
struct bed *exp = be->val;
struct binElement *subList = binKeeperFind(rangeBk,
exp->chromStart, exp->chromEnd);
if (slCount(subList) > 1)
{
struct binElement *sub;
for (sub = subList; sub != NULL; sub = sub->next)
{
struct bed *range = sub->val;
struct rangeInfo *ri = hashMustFindVal(riHash, range->name);
ri->isSplit = TRUE;
}
}
slFreeList(&subList);
}
/* Output the nice ones: not split and having some expression info. */
for (ri = riList; ri != NULL; ri = ri->next)
{
if (!ri->isSplit)
{
struct bed *range = ri->range;
beList = binKeeperFind(expBk, range->chromStart, range->chromEnd);
if (beList != NULL)
outputAveraged(f, ri, erHash, beList);
slFreeList(&beList);
}
}
/* Clean up time! */
freeHash(&riHash);
genePredFreeList(&knownList);
bedFree(&rangeList);
bedFree(&expList);
slFreeList(&rangeBeList);
slFreeList(&beList);
slFreeList(&riList);
binKeeperFree(&rangeBk);
binKeeperFree(&expBk);
binKeeperFree(&knownBk);
}
