void readCoherentGraph(Graph * inGraph, boolean(*isUnique) (Node * node), double coverage, ReadSet * reads) { IDnum nodeIndex; Node *node; IDnum previousNodeCount = 0; graph = inGraph; listMemory = newRecycleBin(sizeof(PassageMarkerList), 100000); expected_coverage = coverage; sequences = reads->tSequences; velvetLog("Read coherency...\n"); resetNodeStatus(graph); identifyUniqueNodes(isUnique); trimLongReadTips(); previousNodeCount = 0; while (previousNodeCount != nodeCount(graph)) { previousNodeCount = nodeCount(graph); for (nodeIndex = 1; nodeIndex <= nodeCount(graph); nodeIndex++) { node = getNodeInGraph(graph, nodeIndex); if (node == NULL || !getUniqueness(node)) continue; while (uniqueNodesConnect(node)) node = bypass(); node = getTwinNode(node); while (uniqueNodesConnect(node)) node = bypass(); } renumberNodes(graph); } destroyRecycleBin(listMemory); destroyRecycleBin(nodeListMemory); velvetLog("Confronted to %li multiple hits and %li null over %li\n", (long) multCounter, (long) nullCounter, (long) dbgCounter); velvetLog("Read coherency over!\n"); }
// 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"); }