struct hash *allChainsHash(char *fileName)
/* Hash all the chains in a given file by their ids. */
{
struct hash *chainHash = newHash(18);
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct chain *chain;
char chainId[20];
struct lm *lm = chainHash->lm;
struct rbTreeNode **stack;
lmAllocArray(lm, stack, 128);
while ((chain = chainRead(lf)) != NULL)
{
struct indexedChain *ixc;
lmAllocVar(lm, ixc);
ixc->chain = chain;
#ifdef SOON
#endif /* SOON */
ixc->blockTree = rangeTreeNewDetailed(lm, stack);
struct cBlock *block;
for (block = chain->blockList; block != NULL; block = block->next)
{
struct range *r = rangeTreeAdd(ixc->blockTree, block->tStart, block->tEnd);
r->val = block;
}
safef(chainId, sizeof(chainId), "%x", chain->id);
hashAddUnique(chainHash, chainId, ixc);
}
lineFileClose(&lf);
return chainHash;
}
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);
}
struct rbTree *genomeRangeTreeFindOrAddRangeTree(struct genomeRangeTree *tree, char *chrom)
/* Find the rangeTree for this chromosome, or add new chrom and empty rangeTree if not found. */
{
struct hashEl *hel;
hel = hashStore(tree->hash, chrom);
if (hel->val == NULL) /* need to add a new rangeTree */
hel->val = rangeTreeNewDetailed(tree->lm, tree->stack);
return hel->val;
}
void refSeparateButJoined(struct txGraph *graph, FILE *f)
/* Flag graphs that have two non-overlapping refSeqs. */
{
int sourceIx;
boolean foundIt = FALSE;
struct lm *lm = lmInit(0);
struct rbTreeNode **stack;
lmAllocArray(lm, stack, 128);
/* Loop through sources looking for reference type. */
for (sourceIx=0; sourceIx<graph->sourceCount; ++sourceIx)
{
struct txSource *source = &graph->sources[sourceIx];
if (sameString(source->type, refType))
{
/* Create a rangeTree including all exons of source. */
struct rbTree *tree = rangeTreeNewDetailed(lm, stack);
struct txEdge *edge;
for (edge = graph->edgeList; edge != NULL; edge = edge->next)
{
if (edge->type == ggExon && evOfSourceOnList(edge->evList, sourceIx))
rangeTreeAdd(tree, graph->vertices[edge->startIx].position,
graph->vertices[edge->endIx].position);
}
/* Go through remaining reference sources looking for no overlap. */
int i;
for (i=0; i<graph->sourceCount; ++i)
{
if (i == sourceIx)
continue;
struct txSource *s = &graph->sources[i];
if (sameString(s->type, refType))
{
boolean gotOverlap = FALSE;
for (edge = graph->edgeList; edge != NULL; edge = edge->next)
{
if (edge->type == ggExon && evOfSourceOnList(edge->evList, i))
{
if (rangeTreeOverlaps(tree,
graph->vertices[edge->startIx].position,
graph->vertices[edge->endIx].position))
{
gotOverlap = TRUE;
break;
}
}
}
if (!gotOverlap)
{
foundIt = TRUE;
break;
}
}
}
freez(&tree);
}
if (foundIt)
break;
}
if (foundIt)
{
fprintf(f, "%s\t%d\t%d\t%s\t0\t%s\n", graph->tName,
graph->tStart, graph->tEnd, "refJoined", graph->strand);
}
lmCleanup(&lm);
}
