static void snapSoftToCloseHard(struct rbTree *vertexTree, struct rbTree *edgeTree, int maxSnapSize,
int maxUncheckedSnapSize, struct nibTwoCache *seqCache, char *chromName)
/* Snap hard vertices to nearby soft vertices of same type. */
{
struct lm *lm = lmInit(0);
addWaysInAndOut(vertexTree, edgeTree, lm);
struct dlList *vList = sortedListFromTree(vertexTree);
struct dlNode *node;
int snapCount = 0;
for (node = vList->head; !dlEnd(node); node = node->next)
{
if (snapVertex(node, maxSnapSize, maxUncheckedSnapSize, seqCache, chromName))
{
rbTreeRemove(vertexTree, node->val);
++snapCount;
}
}
/* Clean up ways in and out since have removed some nodes. */
for (node = vList->head; !dlEnd(node); node = node->next)
{
struct vertex *v = node->val;
v->waysIn = v->waysOut = NULL;
}
if (snapCount > 0)
{
verbose(3, "Snapped %d close edges, now have %d vertices\n", snapCount, vertexTree->n);
updateForwardedEdges(edgeTree);
}
dlListFree(&vList);
lmCleanup(&lm);
}
static void updateForwardedEdges(struct rbTree *edgeTree)
/* Go through edges, following the movedTo's in the
* vertices if need be. */
{
struct slRef *ref, *refList = rbTreeItems(edgeTree);
int forwardCount = 0;
for (ref = refList; ref != NULL; ref = ref->next)
{
struct edge *edge = ref->val;
struct vertex *start = edge->start, *end = edge->end;
if (start->movedTo || end->movedTo)
{
++forwardCount;
rbTreeRemove(edgeTree, edge);
if (start->movedTo)
edge->start = start->movedTo;
if (end->movedTo)
edge->end = end->movedTo;
mergeOrAddEdge(edgeTree, edge);
}
}
if (forwardCount > 0)
verbose(3, "Forwarded %d edges.\n", forwardCount);
slFreeList(&refList);
}
static void halfConsensusBackward(struct vertex *v,
struct rbTree *vertexTree, struct rbTree *edgeTree,
enum ggVertexType softType, struct lm *lm)
/* Figure out consensus start of all edges end at v that have soft start. */
{
/* Collect a list of all attached softies. */
struct sourceAndPos *list = NULL, *el;
struct slRef *edgeRef;
int softCount = 0;
for (edgeRef = v->waysIn; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *edge = edgeRef->val;
struct vertex *v = edge->start;
if (v->type == softType)
{
struct evidence *ev;
for (ev = edge->evList; ev != NULL; ev = ev->next)
{
lmAllocVar(lm, el);
el->position = ev->start;
el->trustedSource = trustedSource(ev->lb->sourceType);
slAddHead(&list, el);
++softCount;
}
}
}
/* See if have enough elements to make consensus forming
* worthwhile. */
if (softCount > 1)
{
slSort(&list, sourceAndPosCmp);
struct vertex *start = consensusVertex(vertexTree, list, softCount, softType);
for (edgeRef = v->waysIn; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *edge = edgeRef->val;
struct vertex *v = edge->start;
if (v != start && v->type == softType)
{
rbTreeRemove(edgeTree, edge);
verbose(3, "Performing half-hard consensus: moving edge start from %d to %d\n",
edge->start->position, start->position);
edge->start = start;
mergeOrAddEdge(edgeTree, edge); // Will always merge.
}
}
}
}
static struct range *rangeTreeAddValHead(struct rbTree *tree, int start, int end, struct slName **newVal) {
struct range *r, *existing;
struct slName *head;
AllocVar(r);
r->start = start;
r->end = end;
r->val = *newVal;
while ((existing = rbTreeRemove(tree, r))) {
r->start = min(r->start, existing->start);
r->end = max(r->end, existing->end);
head = (struct slName *)(existing->val);
slAddHead(&head, *newVal);
r->val = head;
}
rbTreeAdd(tree, r);
return r;
}
static void removeEmptyEdges(struct rbTree *vertexTree, struct rbTree *edgeTree)
/* Remove edges that are zero or negative in length. */
{
int removeCount = 0;
struct slRef *edgeRef, *edgeRefList = rbTreeItems(edgeTree);
for (edgeRef = edgeRefList; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *edge = edgeRef->val;
if (edge->start->position >= edge->end->position)
{
removeCount += 1;
rbTreeRemove(edgeTree, edge);
}
}
if (removeCount)
removeUnusedVertices(vertexTree, edgeTree);
slFreeList(&edgeRefList);
}
int snapHalfHardBackward(struct vertex *v, struct rbTree *edgeTree,
enum ggVertexType softType, enum ggVertexType hardType)
/* V is a hard vertex. Try to snap soft start vertices connected to v
* to nearest hard vertex connected to v. */
{
int snapCount = 0;
// enum ggVertex otherHardType = (hardType == ggHardStart ? ggHardEnd : ggHardStart);
slSort(&v->waysIn, edgeRefCmpStartRev);
struct slRef *hardRef = v->waysIn, *softRef = v->waysIn;
for (;;)
{
/* Advance softRef to next soft ended edge. */
for (;softRef != NULL; softRef = softRef->next)
{
struct edge *edge = softRef->val;
if (edge->start->type == softType)
break;
}
if (softRef == NULL)
break;
struct edge *softEdge = softRef->val;
/* If hardRef is before softRef (or it's not hard) advance it */
for (;hardRef != NULL; hardRef = hardRef->next)
{
struct edge *edge = hardRef->val;
if (edge->start->type == hardType && edge->start->position <= softEdge->start->position)
break;
}
if (hardRef == NULL)
break;
rbTreeRemove(edgeTree, softEdge);
struct edge *hardEdge = hardRef->val;
verbose(3, "Snapping half-hard edge starting at %d to %d\n", softEdge->start->position,
hardEdge->start->position);
softEdge->start = hardEdge->start;
++snapCount;
mergeOrAddEdge(edgeTree, softEdge);
softRef = softRef->next;
}
if (snapCount > 0)
verbose(3, "Snapped %d reverse\n", snapCount);
return snapCount;
}
struct range *rangeTreeAddVal(struct rbTree *tree, int start, int end, void *val, void *(*mergeVals)(void *existingVal, void *newVal) )
/* Add range to tree, merging with existing ranges if need be.
* If this is a new range, set the value to this val.
* If there are existing items for this range, and if mergeVals function is not null,
* apply mergeVals to the existing values and this new val, storing the result as the val
* for this range (see rangeTreeAddValCount() and rangeTreeAddValList() below for examples). */
{
struct range *r, *existing;
r = lmAlloc(tree->lm, sizeof(*r)); /* alloc new zeroed range */
r->start = start;
r->end = end;
r->val = val;
while ((existing = rbTreeRemove(tree, r)) != NULL)
{
r->start = min(r->start, existing->start);
r->end = max(r->end, existing->end);
if (mergeVals)
r->val = mergeVals(existing->val, r->val);
}
rbTreeAdd(tree, r);
return r;
}
struct fill *fillSpace(struct chrom *chrom, struct space *space,
struct chain *chain, struct cBlock *startBlock,
boolean isQ)
/* Fill in space with chain, remove existing space from chrom,
* and add smaller spaces on either side if big enough. */
{
struct fill *fill;
int s, e;
struct space *lSpace, *rSpace;
if (!innerBounds(startBlock, isQ, space->start, space->end, &s, &e))
return NULL;
assert(s < e);
AllocVar(fill);
fill->start = s;
fill->end = e;
fill->chain = chain;
rbTreeRemove(chrom->spaces, space);
if (s - space->start >= minSpace)
{
AllocVar(lSpace);
lSpace->gap = space->gap;
lSpace->start = space->start;
lSpace->end = s;
rbTreeAdd(chrom->spaces, lSpace);
}
if (space->end - e >= minSpace)
{
AllocVar(rSpace);
rSpace->gap = space->gap;
rSpace->start = e;
rSpace->end = space->end;
rbTreeAdd(chrom->spaces, rSpace);
}
slAddHead(&space->gap->fillList, fill);
return fill;
}
static void removeUnusedVertices(struct rbTree *vertexTree, struct rbTree *edgeTree)
/* Remove vertices not connected to any edges. */
{
/* Get vertex list and clear counts. */
struct slRef *vRef, *vRefList = rbTreeItems(vertexTree);
for (vRef = vRefList; vRef != NULL; vRef = vRef->next)
{
struct vertex *v = vRef->val;
v->count = 0;
}
/* Inc counts of vertices connected to edges. */
rbTreeTraverse(edgeTree, incVertexUses);
/* Remove unused vertices. */
for (vRef = vRefList; vRef != NULL; vRef = vRef->next)
{
struct vertex *v = vRef->val;
if (v->count == 0)
rbTreeRemove(vertexTree, v);
}
slFreeList(&vRefList);
}
static void removeEnclosedDoubleSofts(struct rbTree *vertexTree, struct rbTree *edgeTree,
int maxBleedOver, double singleExonMaxOverlap)
/* Move double-softs that overlap spliced things to a very great extent into
* the spliced things. Also remove tiny double-softs (no more than 2*maxBleedOver). */
{
/* Traverse graph and build up range tree covering spliced exons. For each
* range of overlapping exons, assemble a singly-linked list of all exons in
* the range */
struct rbTree *rangeTree = rangeTreeNew(0);
struct slRef *edgeRef, *edgeRefList = rbTreeItems(edgeTree);
int removedCount = 0;
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 == ggHardStart || end->type == ggHardEnd)
{
rangeTreeAddValList(rangeTree, start->position, end->position, edge);
}
}
/* Traverse graph yet one more time looking for doubly-soft exons
* that are overlapping the spliced exons. */
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)
{
int s = start->position;
int e = end->position;
int size = e - s;
if (size <= maxBleedOver+maxBleedOver)
{
/* Tiny case, just remove edge and forget it. */
verbose(3, "Removing tiny double-soft edge from %d to %d\n", s, e);
rbTreeRemove(edgeTree, edge);
++removedCount;
}
else
{
/* Normal case, look for exon list that encloses us, and
* if any single exon in that list encloses us, merge into it. */
int splicedOverlap = rangeTreeOverlapSize(rangeTree, s, e);
if (splicedOverlap > 0 && splicedOverlap > singleExonMaxOverlap*size)
{
if (!trustedEdge(edge))
{
/* Once we find a range that overlaps the doubly-soft edge, find
* (half-hard or better) edge from that range that encloses the
* doubly soft edge. */
struct range *r = rangeTreeMaxOverlapping(rangeTree, s, e);
struct edge *nextEdge, *edgeList = r->val;
struct edge *enclosingEdge = NULL;
for (nextEdge = edgeList; edgeList != NULL; edgeList = edgeList->next)
{
if (encloses(nextEdge, edge))
{
enclosingEdge = nextEdge;
}
}
if (enclosingEdge != NULL)
{
enclosingEdge->evList = slCat(enclosingEdge->evList, edge->evList);
edge->evList = NULL;
verbose(3, "Removing doubly-soft edge %d-%d, reassigning to %d-%d\n",
s, e, enclosingEdge->start->position,
enclosingEdge->end->position);
rbTreeRemove(edgeTree, edge);
++removedCount;
}
}
}
}
}
}
/* Clean up and go home. */
if (removedCount > 0)
removeUnusedVertices(vertexTree, edgeTree);
for (edgeRef = edgeRefList; edgeRef != NULL; edgeRef = edgeRef->next)
{
struct edge *nextEdge, *edge = edgeRef->val;
while (edge != NULL)
{
nextEdge = edge->next;
edge->next = NULL;
edge = nextEdge;
}
}
slFreeList(&edgeRefList);
rbTreeFree(&rangeTree);
}
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);
}