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");
}
