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");
}
void dfh_deleteheap(DFibHeap * h)
{
destroyRecycleBin(h->nodeMemory);
if (h->dfh_cons != NULL)
free(h->dfh_cons);
free(h);
}
void destroyAllSplayTrees()
{
#ifdef OPENMP
destroyRecycleBinArray(treeMemory);
#else
destroyRecycleBin(treeMemory);
#endif
treeMemory = NULL;
}
static void cleanMemory()
{
velvetLog("Cleaning memory\n");
cleanScaffoldMemory();
destroyRecycleBin(nodeListMemory);
nodeListMemory = NULL;
free(localScaffold);
}
static void destroySmallNodeListMemmory(void)
{
if (smallNodeListMemory != NULL)
{
#ifdef OPENMP
destroyRecycleBinArray(smallNodeListMemory);
#else
destroyRecycleBin(smallNodeListMemory);
#endif
smallNodeListMemory = NULL;
}
}
void cleanTranscriptMemory(Locus * loci, IDnum locusCount)
{
IDnum index;
Transcript *transcript;
for (index = 0; index < locusCount; index++) {
Locus * locus = getLocus(loci, index);
for (transcript = getTranscript(locus); transcript;
transcript = transcript->next) {
free(transcript->contigs);
free(transcript->distances);
}
}
destroyRecycleBin(transcriptMemory);
transcriptMemory = NULL;
}
static void fillUpGraph(ReadSet * reads,
KmerOccurenceTable * kmerOccurences, Graph * graph,
boolean readTracking, boolean double_strand)
{
IDnum readIndex;
Category category;
resetNodeStatus(graph);
for (readIndex = 0; readIndex < reads->readCount; readIndex++) {
category = reads->categories[readIndex];
ghostThreadSequenceThroughGraph(reads->
tSequences[readIndex],
kmerOccurences,
graph, readIndex + 1,
category,
readTracking, double_strand);
}
createNodeReadStartArrays(graph);
for (readIndex = 0; readIndex < reads->readCount; readIndex++) {
category = reads->categories[readIndex];
if (readIndex % 100000 == 0)
printf("Threading through reads %d / %d\n",
readIndex, reads->readCount);
threadSequenceThroughGraph(reads->tSequences[readIndex],
kmerOccurences,
graph, readIndex + 1, category,
readTracking, double_strand);
}
orderNodeReadStartArrays(graph);
if (smallNodeListMemory != NULL)
destroyRecycleBin(smallNodeListMemory);
free(kmerOccurences->kmerTable);
free(kmerOccurences->accelerationTable);
free(kmerOccurences);
}
