static stList *mergeSimpleCycles2(stList *chosenEdges,
stList *nonZeroWeightAdjacencyEdges, stSortedSet *allAdjacencyEdges,
stList *stubEdges, stList *chainEdges) {
/*
* Returns a new set of chosen edges, modified by adjacency switches such that every simple cycle
* contains at least one stub edge.
*/
/*
* Calculate components.
*/
stList *components = getComponents2(chosenEdges, stubEdges, chainEdges);
/*
* Divide the components by the presence of one or more stub edges.
*/
stSortedSet *stubEdgesSet = stList_getSortedSet(stubEdges,
(int(*)(const void *, const void *)) stIntTuple_cmpFn);
stList *stubContainingComponents = stList_construct();
stList *stubFreeComponents = stList_construct();
for (int64_t i = 0; i < stList_length(components); i++) {
stList *component = stList_get(components, i);
stList_append(
intersectionSize(stubEdgesSet, component) > 0 ? stubContainingComponents
: stubFreeComponents, component);
}
assert(stList_length(stubContainingComponents) > 0);
stSortedSet_destruct(stubEdgesSet);
/*
* Merge the stub containing components into one 'global' component
*/
stList *globalComponent = stList_join(stubContainingComponents);
stList_destruct(stubContainingComponents);
/*
* Remove the stub/chain edges from the components.
*/
stList_append(stubFreeComponents, globalComponent);
stList *adjacencyOnlyComponents = getStubAndChainEdgeFreeComponents(
stubFreeComponents, stubEdges, chainEdges);
stList_destruct(stubFreeComponents);
stList_destruct(globalComponent);
stList_destruct(components); //We only clean this up now, as this frees the components it contains.
/*
* Merge stub free components into the others.
*/
stList *updatedChosenEdges = mergeSimpleCycles(adjacencyOnlyComponents,
nonZeroWeightAdjacencyEdges, allAdjacencyEdges);
stList_destruct(adjacencyOnlyComponents);
return updatedChosenEdges;
}
void tAddTrf(struct chainNet *net, struct cnFill *fillList, struct rbTree *tree)
/* Add t simple repeats's to all things underneath fillList. */
{
struct cnFill *fill;
for (fill = fillList; fill != NULL; fill = fill->next)
{
int s = liftStart(net->name, fill->tStart, liftHashT);
fill->tTrf = intersectionSize(tree, s, s + fill->tSize);
if (fill->children)
tAddTrf(net, fill->children, tree);
}
}
void qAddTrf(struct chainNet *net, struct cnFill *fillList, struct hash *qChromHash)
/* Add q new repeats to all things underneath fillList. */
{
struct cnFill *fill;
for (fill = fillList; fill != NULL; fill = fill->next)
{
struct chrom *qChrom = getQChrom(fill->qName, qChromHash);
int s = liftStart(fill->qName, fill->qStart, liftHashQ);
fill->qTrf = intersectionSize(qChrom->trf, s, s + fill->qSize);
if (fill->children)
qAddTrf(net, fill->children, qChromHash);
}
}
void qAddN(struct chainNet *net, struct cnFill *fillList, struct hash *qChromHash)
/* Add qN's to all gaps underneath fillList. */
{
struct cnFill *fill;
for (fill = fillList; fill != NULL; fill = fill->next)
{
struct chrom *qChrom = getQChrom(fill->qName, qChromHash);
struct rbTree *tree = qChrom->nGaps;
int s = liftStart(fill->qName, fill->qStart, liftHashQ);
fill->qN = intersectionSize(tree, s, s + fill->qSize);
if (fill->children)
qAddN(net, fill->children, qChromHash);
}
}