static struct bed* subset_beds(char* sectionString, struct bed** pRegions, struct hash* chromHash)
/* in the situation where both a regions bed file is given AND the filename specifies subsections, */
/* intersect the two. For simplictity sake, */
{
struct bed* fname_ranges = parseSectionString(sectionString, chromHash);
struct bed* bed;
struct bed* subset = NULL;
struct bed* regions = *pRegions;
slSort(&fname_ranges, bedCmp);
bed = fname_ranges;
while (bed != NULL) {
/* each iteration of the loop should be a separate chrom */
struct bed* region;
struct rbTree* tree = rangeTreeNew();
while ((bed != NULL) && (bed->next != NULL) && (sameString(bed->chrom, bed->next->chrom))) {
rangeTreeAdd(tree, bed->chromStart, bed->chromEnd);
bed = bed->next;
}
rangeTreeAdd(tree, bed->chromStart, bed->chromEnd);
/* now we're at a point that we're dealing only with one chromosome. */
for (region = regions; region != NULL; region = region->next) {
if (sameString(region->chrom, bed->chrom) && rangeTreeOverlaps(tree, region->chromStart, region->chromEnd)
&& rangeTreeFindEnclosing(tree, region->chromStart, region->chromEnd)) {
struct bed* clone = cloneBed(region);
slAddHead(&subset, clone);
} else if (sameString(region->chrom, bed->chrom) && rangeTreeOverlaps(tree, region->chromStart, region->chromEnd))
errAbort("range specified in file overlaps but is not contained by range specified on command-line");
}
rangeTreeFree(&tree);
bed = bed->next;
}
if (subset == NULL) {
errAbort("no ranges specified in file were contained in ranges specified on command-line");
}
slReverse(&subset);
bedFreeList(&fname_ranges);
bedFreeList(pRegions);
return subset;
}
static void mergeDoubleSofts(struct rbTree *vertexTree, struct rbTree *edgeTree)
/* Merge together overlapping edges with soft ends. */
{
struct mergedEdge
/* Hold together info on a merged edge. */
{
struct evidence *evidence;
};
/* Traverse graph and build up range tree. Each node in the range tree
* will represent the bounds of coordinates of overlapping double softs */
struct rbTree *rangeTree = rangeTreeNew(0);
struct slRef *edgeRef, *edgeRefList = rbTreeItems(edgeTree);
for (edgeRef = edgeRefList; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *edge = edgeRef->val;
struct vertex *start = edge->start;
struct vertex *end = edge->end;
if (start->type == ggSoftStart && end->type == ggSoftEnd)
rangeTreeAdd(rangeTree, start->position, end->position);
}
/* Traverse graph again merging edges */
for (edgeRef = edgeRefList; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *edge = edgeRef->val;
struct vertex *start= edge->start;
struct vertex *end = edge->end;
if (start->type == ggSoftStart && end->type == ggSoftEnd)
{
struct range *r = rangeTreeFindEnclosing(rangeTree,
start->position, end->position);
assert(r != NULL);
/* At this point, r represents the bounds of a double-soft
* region that encompasses this edge. Collect the set of
* evidence of edges overlapping this range */
struct mergedEdge *mergeEdge = r->val;
if (mergeEdge == NULL)
{
lmAllocVar(rangeTree->lm, mergeEdge);
r->val = mergeEdge;
}
mergeEdge->evidence = slCat(edge->evList, mergeEdge->evidence);
verbose(3, "Merging doubly-soft edge (%d,%d) into range (%d,%d)\n",
start->position, end->position, r->start, r->end);
edge->evList = NULL;
rbTreeRemove(edgeTree, edge);
}
}
/* Traverse merged edge list, making a single edge from each range. At this point,
* each range will have some evidence attached to it, from each of the double softs
* that fall within the range. From all of this evidence, make a single consensus edge */
struct range *r;
struct lm *lm = lmInit(0);
for (r = rangeTreeList(rangeTree); r != NULL; r = r->next)
{
struct mergedEdge *mergedEdge = r->val;
struct edge *edge = edgeFromConsensusOfEvidence(vertexTree, mergedEdge->evidence, lm);
if (edge != NULL)
rbTreeAdd(edgeTree, edge);
verbose(3, "Deriving edge (%d,%d) from all the double softs in range (%d,%d)\n",
edge->start->position, edge->end->position, r->start, r->end);
}
/* Clean up and go home. */
lmCleanup(&lm);
removeUnusedVertices(vertexTree, edgeTree);
slFreeList(&edgeRefList);
rbTreeFree(&rangeTree);
}
