static Event *allocateEvent()
{
if (eventMemory == NULL)
eventMemory = newRecycleBin(sizeof(Event), BLOCK_SIZE);
return allocatePointer(eventMemory);
}
static Mask *allocateMask(SequencesWriter *seqWriteInfo)
{
if (seqWriteInfo->m_maskMemory == NULL)
seqWriteInfo->m_maskMemory = newRecycleBin(sizeof(Mask), 10000);
return (Mask *) allocatePointer(seqWriteInfo->m_maskMemory);
}
static Mask *allocateMask()
{
if (maskMemory == NULL)
maskMemory = newRecycleBin(sizeof(Mask), 10000);
return (Mask *) allocatePointer(maskMemory);
}
static Connection *allocateConnection()
{
if (connectionMemory == NULL)
connectionMemory =
newRecycleBin(sizeof(Connection), BLOCK_SIZE);
return allocatePointer(connectionMemory);
}
Transcript *allocateTranscript()
{
if (transcriptMemory == NULL)
transcriptMemory =
newRecycleBin(sizeof(Transcript), BLOCK_SIZE);
return (Transcript*)allocatePointer(transcriptMemory);
}
static SmallNodeList *allocateSmallNodeList()
{
if (smallNodeListMemory == NULL)
smallNodeListMemory =
newRecycleBin(sizeof(SmallNodeList), BLOCKSIZE);
return allocatePointer(smallNodeListMemory);
}
static NodeList *allocateNodeList()
{
if (nodeListMemory == NULL)
nodeListMemory =
newRecycleBin(sizeof(NodeList), BLOCK_SIZE);
return (NodeList*)allocatePointer(nodeListMemory);
}
static RBConnection *allocateRBConnection()
{
if (nodeListMemory == NULL)
nodeListMemory =
newRecycleBin(sizeof(RBConnection), BLOCKSIZE);
return allocatePointer(nodeListMemory);
}
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");
}
/*
* Public Heap Functions
*/
DFibHeap *dfh_makekeyheap()
{
DFibHeap *n;
if ((n = (DFibHeap*)malloc(sizeof *n)) == NULL)
return NULL;
n->nodeMemory = newRecycleBin(sizeof(DFibHeapNode), BLOCKSIZE);
n->dfh_n = 0;
n->dfh_Dl = -1;
n->dfh_cons = NULL;
n->dfh_min = NULL;
n->dfh_root = NULL;
return n;
}
static SplayNode *allocateSplayNode()
{
#ifdef OPENMP
#ifdef DEBUG
if (treeMemory == NULL)
{
velvetLog("The memory for splay trees seems uninitialised, "
"this is probably a bug, aborting.\n");
abort();
}
#endif
return allocatePointer(getRecycleBinInArray(treeMemory,
omp_get_thread_num()));
#else
if (treeMemory == NULL)
treeMemory = newRecycleBin(sizeof(SplayNode), CHUNKSIZE);
return allocatePointer(treeMemory);
#endif
}
static SmallNodeList *allocateSmallNodeList()
{
#ifdef OPENMP
#ifdef DEBUG
if (smallNodeListMemory == NULL)
{
velvetLog("The memory for small nodes seems uninitialised, "
"this is probably a bug, aborting.\n");
abort();
}
#endif
return allocatePointer(getRecycleBinInArray(smallNodeListMemory,
omp_get_thread_num()));
#else
if (smallNodeListMemory == NULL)
smallNodeListMemory = newRecycleBin(sizeof(SmallNodeList), BLOCKSIZE);
return allocatePointer(smallNodeListMemory);
#endif
}
