void peakClusterMakerAddFromSource(struct peakClusterMaker *maker, struct peakSource *source)
/* Read through data source and add items to it to rangeTrees in maker */
{
struct hash *chromHash = maker->chromHash;
struct lineFile *lf = lineFileOpen(source->dataSource, TRUE);
struct lm *lm = chromHash->lm; /* Local memory pool - share with hash */
char *row[source->minColCount];
struct peakItem *item;
char *line;
while (lineFileNextReal(lf, &line))
{
char *asciiLine = lmCloneString(lm, line);
int wordCount = chopByWhite(line, row, source->minColCount);
lineFileExpectAtLeast(lf, source->minColCount, wordCount);
char *chrom = row[source->chromColIx];
struct hashEl *hel = hashLookup(chromHash, chrom);
if (hel == NULL)
{
struct rbTree *tree = rangeTreeNewDetailed(lm, maker->stack);
hel = hashAdd(chromHash, chrom, tree);
}
struct rbTree *tree = hel->val;
lmAllocVar(lm, item);
item->chrom = hel->name;
item->chromStart = sqlUnsigned(row[source->startColIx]);
item->chromEnd = sqlUnsigned(row[source->endColIx]);
item->score = sqlDouble(row[source->scoreColIx]) * source->normFactor;
if (item->score > 1000) item->score = 1000;
item->source = source;
item->asciiLine = asciiLine;
rangeTreeAddValList(tree, item->chromStart, item->chromEnd, item);
}
lineFileClose(&lf);
}
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);
}
