void processOneGraph(struct txGraph *txg, struct hash *weightHash, double threshold,
char *outType, FILE *f)
/* Write out edges for one graph. */
{
struct txEdge *edge;
struct txEdgeBed e;
ZeroVar(&e);
e.chrom = txg->tName;
for (edge = txg->edgeList; edge != NULL; edge = edge->next)
{
double weight = weightOfEvidence(txg, edge->evList, weightHash);
if (weight >= threshold)
{
struct txVertex *start = &txg->vertices[edge->startIx];
struct txVertex *end = &txg->vertices[edge->endIx];
e.chromStart = start->position;
e.chromEnd = end->position;
e.name = outType;
e.score = edge->evCount;
e.strand[0] = txg->strand[0];
e.startType[0] = ggVertexTypeAsString(start->type)[0];
e.type = edge->type;
e.endType[0] = ggVertexTypeAsString(end->type)[0];
txEdgeBedTabOut(&e, f);
}
}
}
void writeOverlappingEdges(
enum ggEdgeType edgeType, struct txGraph *inGraph,
int inStart, int mappedStart, enum ggVertexType startType, boolean startMappedExact,
int inEnd, int mappedEnd, enum ggVertexType endType, boolean endMappedExact,
struct txGraph *orthoGraph, boolean orthoRev, int mappedCoverage, FILE *f)
/* Write edges of graph that overlap correctly to f */
{
if (startType == ggSoftStart || startType == ggSoftEnd || startMappedExact)
{
if (endType == ggSoftStart || endType == ggSoftEnd || endMappedExact)
{
struct txEdge *edge;
for (edge = orthoGraph->edgeList; edge != NULL; edge = edge->next)
{
if (edge->type == edgeType)
{
int orthoStartIx = edge->startIx;
int orthoStart = orthoGraph->vertices[orthoStartIx].position;
enum ggVertexType orthoStartType = orthoGraph->vertices[orthoStartIx].type;
int orthoEndIx = edge->endIx;
int orthoEnd = orthoGraph->vertices[orthoEndIx].position;
enum ggVertexType orthoEndType = orthoGraph->vertices[orthoEndIx].type;
int overlap = rangeIntersection(mappedStart, mappedEnd, orthoStart, orthoEnd);
if (overlap > 0)
{
enum ggVertexType rStartType = startType, rEndType = endType;
if (orthoRev)
{
rStartType = endType;
rEndType = startType;
}
if (rStartType == ggSoftStart || rStartType == ggSoftEnd || mappedStart == orthoStart)
{
if (rEndType == ggSoftStart || rEndType == ggSoftEnd || mappedEnd == orthoEnd)
{
/* Compute score that depends on how much start/end have wobbled. */
int mappedOverlapScore = 1000 * overlap/(mappedEnd - mappedStart);
int orthoOverlapScore = 1000 * overlap/(orthoEnd - orthoStart);
int overlapScore = min(mappedOverlapScore, orthoOverlapScore);
int coverageScore = 1000 * mappedCoverage/(inEnd - inStart);
/* Write out bed fields. */
fprintf(f, "%s\t%d\t%d\t", inGraph->tName, inStart, inEnd);
fprintf(f, "%s\t", orthoGraph->name);
fprintf(f, "%d\t", coverageScore);
fprintf(f, "%s\t", inGraph->strand);
/* Write out edge and vertex type info. */
fprintf(f, "%s\t", ggVertexTypeAsString(startType));
fprintf(f, "%s\t", (edgeType == ggExon ? "exon" : "intron"));
fprintf(f, "%s\t", ggVertexTypeAsString(endType));
/* Write out mouse info. */
fprintf(f, "%s\t%d\t%d\t", orthoGraph->tName, mappedStart, mappedEnd);
fprintf(f, "%s\t", inGraph->name);
fprintf(f, "%d\t", overlapScore);
fprintf(f, "%s\t", orthoGraph->strand);
fprintf(f, "%s\t", ggVertexTypeAsString(orthoStartType));
fprintf(f, "%s\t", ggVertexTypeAsString(orthoEndType));
fprintf(f, "%d\t", orthoStart);
fprintf(f, "%d\n", orthoEnd);
}
}
}
}
}
}
}
}
