// Detects sequences that could be simplified through concatentation
// Iterates till graph cannot be more simplified
// Useless nodes are freed from memory and remaining ones are renumbered
void concatenateGraph(Graph * graph)
{
IDnum nodeIndex;
Node *node, *twin;
velvetLog("Concatenation...\n");
for (nodeIndex = 1; nodeIndex < nodeCount(graph); nodeIndex++) {
node = getNodeInGraph(graph, nodeIndex);
if (node == NULL)
continue;
twin = getTwinNode(node);
while (simpleArcCount(node) == 1
&&
simpleArcCount(getTwinNode
(getDestination(getArc(node)))) ==
1) {
if (getDestination(getArc(node)) == twin
|| getDestination(getArc(node)) == node)
break;
concatenateStringOfNodes(node,
graph);
}
while (simpleArcCount(twin) == 1
&&
simpleArcCount(getTwinNode
(getDestination(getArc(twin)))) ==
1) {
if (getDestination(getArc(twin)) == node
|| getDestination(getArc(twin)) == twin)
break;
concatenateStringOfNodes(twin,
graph);
}
}
renumberNodes(graph);
sortGapMarkers(graph);
velvetLog("Concatenation over!\n");
}
void exploitShortReadPairs(Graph * argGraph,
ReadSet * reads,
boolean * dubious,
boolean * shadows,
boolean force_jumps)
{
boolean modified = true;
graph = argGraph;
if (!readStartsAreActivated(graph))
return;
velvetLog("Starting pebble resolution...\n");
resetNodeStatus(graph);
// Prepare scaffold
buildScaffold(graph, reads, dubious, shadows);
// Prepare graph
prepareGraphForLocalCorrections(graph);
// Prepare local scaffold
localScaffold =
callocOrExit(2 * nodeCount(graph) + 1, MiniConnection);
// Loop until convergence
while (modified)
modified = expandLongNodes(force_jumps);
// Clean up memory
cleanMemory();
deactivateLocalCorrectionSettings();
sortGapMarkers(graph);
velvetLog("Pebble done.\n");
}
