Esempi in C++ (Cpp) per orderNodeReadStartArrays

Esempio n. 1

File: graphReConstruction.c Progetto: macmanes/velvet

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);
}

Esempio n. 2

File: graphReConstruction.c Progetto: GunioRobot/velvet

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);
}