// The full monty, wrapped up in one function
PreGraph *newPreGraph_pg(RoadMapArray * rdmapArray, SequencesReader *seqReadInfo)
{
int WORDLENGTH = rdmapArray->WORDLENGTH;
IDnum sequenceCount = rdmapArray->length;
IDnum *markerCounters = callocOrExit(sequenceCount + 1, IDnum);
IDnum *chains = callocOrExit(sequenceCount + 1, IDnum);
InsertionMarker *insertionMarkers;
InsertionMarker *veryLastMarker;
PreGraph *preGraph =
emptyPreGraph_pg(sequenceCount, rdmapArray->referenceCount, rdmapArray->WORDLENGTH, rdmapArray->double_strand);
velvetLog("Creating insertion markers\n");
setInsertionMarkers(rdmapArray, markerCounters, &veryLastMarker,
&insertionMarkers);
velvetLog("Counting preNodes\n");
countPreNodes(rdmapArray, preGraph, markerCounters,
insertionMarkers, veryLastMarker);
velvetLog("%li preNodes counted, creating them now\n",
(long) preNodeCount_pg(preGraph));
createPreNodes(rdmapArray, preGraph, markerCounters,
insertionMarkers, veryLastMarker, chains,
seqReadInfo, WORDLENGTH);
velvetLog("Adjusting marker info...\n");
convertInsertionMarkers(insertionMarkers, veryLastMarker, chains);
#ifdef _OPENMP
createNodeLocks(preGraph);
#endif
velvetLog("Connecting preNodes\n");
connectPreNodes(rdmapArray, preGraph, chains);
velvetLog("Cleaning up memory\n");
cleanUpMemory(preGraph, rdmapArray, chains);
#ifdef _OPENMP
free(nodeLocks);
nodeLocks = NULL;
#endif
velvetLog("Done creating preGraph\n");
return preGraph;
}
static void fillUpGraph(ReadSet * reads,
KmerOccurenceTable * kmerTable,
Graph * graph,
boolean readTracking,
boolean double_strand,
ReferenceMapping * referenceMappings,
Coordinate referenceMappingCount,
IDnum refCount,
char * roadmapFilename)
{
IDnum readIndex;
RoadMapArray *roadmap = NULL;
Coordinate *annotationOffset = NULL;
struct timeval start, end, diff;
if (referenceMappings)
{
roadmap = importRoadMapArray(roadmapFilename);
annotationOffset = callocOrExit(reads->readCount, Coordinate);
for (readIndex = 1; readIndex < reads->readCount; readIndex++)
annotationOffset[readIndex] = annotationOffset[readIndex - 1]
+ getAnnotationCount(getRoadMapInArray(roadmap, readIndex - 1));
}
resetNodeStatus(graph);
// Allocate memory for the read pairs
if (!readStartsAreActivated(graph))
activateReadStarts(graph);
gettimeofday(&start, NULL);
#ifdef OPENMP
initSmallNodeListMemory();
createNodeLocks(graph);
#pragma omp parallel for
#endif
for (readIndex = refCount; readIndex < reads->readCount; readIndex++)
{
Annotation * annotations = NULL;
IDnum annotationCount = 0;
Category category;
boolean second_in_pair;
if (readIndex % 1000000 == 0)
velvetLog("Ghost Threading through reads %ld / %ld\n",
(long) readIndex, (long) reads->readCount);
category = reads->categories[readIndex];
second_in_pair = reads->categories[readIndex] & 1 && isSecondInPair(reads, readIndex);
if (referenceMappings)
{
annotationCount = getAnnotationCount(getRoadMapInArray(roadmap, readIndex));
annotations = getAnnotationInArray(roadmap->annotations, annotationOffset[readIndex]);
}
ghostThreadSequenceThroughGraph(getTightStringInArray(reads->tSequences, readIndex),
kmerTable,
graph, readIndex + 1,
category,
readTracking, double_strand,
referenceMappings, referenceMappingCount,
refCount, annotations, annotationCount,
second_in_pair);
}
createNodeReadStartArrays(graph);
gettimeofday(&end, NULL);
timersub(&end, &start, &diff);
velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec);
gettimeofday(&start, NULL);
#ifdef OPENMP
int threads = omp_get_max_threads();
if (threads > 32)
threads = 32;
#pragma omp parallel for num_threads(threads)
#endif
for (readIndex = 0; readIndex < reads->readCount; readIndex++)
{
Annotation * annotations = NULL;
IDnum annotationCount = 0;
Category category;
boolean second_in_pair;
if (readIndex % 1000000 == 0)
velvetLog("Threading through reads %li / %li\n",
(long) readIndex, (long) reads->readCount);
category = reads->categories[readIndex];
second_in_pair = reads->categories[readIndex] % 2 && isSecondInPair(reads, readIndex);
if (referenceMappings)
{
annotationCount = getAnnotationCount(getRoadMapInArray(roadmap, readIndex));
annotations = getAnnotationInArray(roadmap->annotations, annotationOffset[readIndex]);
}
threadSequenceThroughGraph(getTightStringInArray(reads->tSequences, readIndex),
kmerTable,
graph, readIndex + 1, category,
readTracking, double_strand,
referenceMappings, referenceMappingCount,
refCount, annotations, annotationCount, second_in_pair);
}
gettimeofday(&end, NULL);
timersub(&end, &start, &diff);
velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec);
#ifdef OPENMP
free(nodeLocks);
nodeLocks = NULL;
#endif
if (referenceMappings)
{
destroyRoadMapArray(roadmap);
free (annotationOffset);
}
orderNodeReadStartArrays(graph);
destroySmallNodeListMemmory();
destroyKmerOccurenceTable(kmerTable);
}