예제 #1
0
static void threadSequenceThroughGraph(TightString * tString,
				       KmerOccurenceTable * kmerTable,
				       Graph * graph,
				       IDnum seqID, Category category,
				       boolean readTracking,
				       boolean double_strand,
				       ReferenceMapping * referenceMappings,
				       Coordinate referenceMappingCount,
				       IDnum refCount,
				       Annotation * annotations,
				       IDnum annotationCount,
				       boolean second_in_pair)
{
	Kmer word;
	Kmer antiWord;
	Coordinate readNucleotideIndex;
	Coordinate kmerIndex;
	KmerOccurence *kmerOccurence;
	int wordLength = getWordLength(graph);

	PassageMarkerI marker = NULL_IDX;
	PassageMarkerI previousMarker = NULL_IDX;
	Node *node = NULL;
	Node *previousNode = NULL;
	Coordinate coord = 0;
	Coordinate previousCoord = 0;
	Nucleotide nucleotide;
	boolean reversed;

	IDnum refID;
	Coordinate refCoord = 0;
	ReferenceMapping * refMap;
	Annotation * annotation = annotations;
	Coordinate index = 0;
	Coordinate uniqueIndex = 0;
	Coordinate annotIndex = 0;
	IDnum annotCount = 0;
	SmallNodeList * nodePile = NULL;

	// Neglect any string shorter than WORDLENGTH :
	if (getLength(tString) < wordLength)
		return;

	clearKmer(&word);
	clearKmer(&antiWord);

	// Fill in the initial word : 
	for (readNucleotideIndex = 0;
	     readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
		nucleotide = getNucleotide(readNucleotideIndex, tString);
		pushNucleotide(&word, nucleotide);
		if (double_strand || second_in_pair) {
#ifdef COLOR
			reversePushNucleotide(&antiWord, nucleotide);
#else
			reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
		}
	}

	// Go through sequence
	while (readNucleotideIndex < getLength(tString)) {
		nucleotide = getNucleotide(readNucleotideIndex++, tString);
		pushNucleotide(&word, nucleotide);
		if (double_strand || second_in_pair) {
#ifdef COLOR
			reversePushNucleotide(&antiWord, nucleotide);
#else
			reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
		}

		// Update annotation if necessary
		if (annotCount < annotationCount && annotIndex == getAnnotationLength(annotation)) {
			annotation = getNextAnnotation(annotation);
			annotCount++;
			annotIndex = 0;
		}

		// Search for reference mapping
		if (category == REFERENCE) {
			if (referenceMappings) 
				refMap = findReferenceMapping(seqID, index, referenceMappings, referenceMappingCount);
			else 
				refMap = NULL;

			if (refMap) {
				node = getNodeInGraph(graph, refMap->nodeID);
				if (refMap->nodeID > 0) {
					coord = refMap->nodeStart + (index - refMap->referenceStart);
				} else {
					coord = getNodeLength(node) - refMap->nodeStart - refMap->length + (index - refMap->referenceStart);
				}
			} else  {
				node = NULL;
				if (previousNode)
					break;
			}
		}
		// Search for reference-based mapping
		else if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation) && getAnnotSequenceID(annotation) <= refCount && getAnnotSequenceID(annotation) >= -refCount) {
			refID = getAnnotSequenceID(annotation);
			if (refID > 0)
				refCoord = getStart(annotation) + annotIndex; 
			else
				refCoord = getStart(annotation) - annotIndex; 
			
			refMap = findReferenceMapping(refID, refCoord, referenceMappings, referenceMappingCount);
			// If success
			if (refMap) {
				if (refID > 0) {
					node = getNodeInGraph(graph, refMap->nodeID);
					if (refMap->nodeID > 0) {
						coord = refMap->nodeStart + (refCoord - refMap->referenceStart);
					} else {
						coord = getNodeLength(node) - refMap->nodeStart - refMap->length + (refCoord - refMap->referenceStart);
					}
				} else {
					node = getNodeInGraph(graph, -refMap->nodeID);
					if (refMap->nodeID > 0) {
						coord =  getNodeLength(node) - refMap->nodeStart - (refCoord - refMap->referenceStart) - 1;
					} else {
						coord = refMap->nodeStart + refMap->length - (refCoord - refMap->referenceStart) - 1;
					}
				}
			} else  {
				node = NULL;
				if (previousNode)
					break;
			}
		}		
		// Search in table
		else {
			reversed = false;
			if (double_strand) {
				if (compareKmers(&word, &antiWord) <= 0) {
					kmerOccurence =
					findKmerInKmerOccurenceTable(&word,
								       kmerTable);
				} else { 
					kmerOccurence =
					       findKmerInKmerOccurenceTable(&antiWord,
						kmerTable);
					reversed = true;
				}
			} else {
				if (!second_in_pair) {
					kmerOccurence =
					findKmerInKmerOccurenceTable(&word,
								       kmerTable);
				} else { 
					kmerOccurence =
					       findKmerInKmerOccurenceTable(&antiWord,
						kmerTable);
					reversed = true;
				}
			}
			
			if (kmerOccurence) {
				if (!reversed) {
					node = getNodeInGraph(graph, getKmerOccurenceNodeID(kmerOccurence));
					coord = getKmerOccurencePosition(kmerOccurence);
				} else {
					node = getNodeInGraph(graph, -getKmerOccurenceNodeID(kmerOccurence));
					coord = getNodeLength(node) - getKmerOccurencePosition(kmerOccurence) - 1;
				}
			} else {
				node = NULL;
				if (previousNode) 
					break;
			}
		}

		// Increment positions
		if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation)) 
			annotIndex++;
		else
			uniqueIndex++;

		// Fill in graph
		if (node)
		{
#ifdef OPENMP
			lockNode(node);
#endif
			kmerIndex = readNucleotideIndex - wordLength;

			if (previousNode == node
			    && previousCoord == coord - 1) {
				if (category / 2 >= CATEGORIES) {
					setPassageMarkerFinish(marker,
							       kmerIndex +
							       1);
					setFinishOffset(marker,
							getNodeLength(node)
							- coord - 1);
				} else {
#ifndef SINGLE_COV_CAT
					incrementVirtualCoverage(node, category / 2, 1);
					incrementOriginalVirtualCoverage(node, category / 2, 1);
#else
					incrementVirtualCoverage(node, 1);
#endif
				}
#ifdef OPENMP
				unLockNode(node);
#endif
			} else {
				if (category / 2 >= CATEGORIES) {
					marker =
					    newPassageMarker(seqID,
							     kmerIndex,
							     kmerIndex + 1,
							     coord,
							     getNodeLength
							     (node) -
							     coord - 1);
					transposePassageMarker(marker,
							       node);
					connectPassageMarkers
					    (previousMarker, marker,
					     graph);
					previousMarker = marker;
				} else {
					if (readTracking) {
						if (!isNodeMemorized(node, nodePile)) {
							addReadStart(node,
								     seqID,
								     coord,
								     graph,
								     kmerIndex);
							memorizeNode(node, &nodePile);
						} else {
							blurLastShortReadMarker
							    (node, graph);
						}
					}

#ifndef SINGLE_COV_CAT
					incrementVirtualCoverage(node, category / 2, 1);
					incrementOriginalVirtualCoverage(node, category / 2, 1);
#else
					incrementVirtualCoverage(node, 1);
#endif
				}
#ifdef OPENMP
				lockTwoNodes(node, previousNode);
#endif
				createArc(previousNode, node, graph);
#ifdef OPENMP
				unLockTwoNodes(node, previousNode);
#endif
			}

			previousNode = node;
			previousCoord = coord;
		}
		index++;
	}

	if (readTracking && category / 2 < CATEGORIES)
		unMemorizeNodes(&nodePile);
}
예제 #2
0
static void threadSequenceThroughGraph(TightString * tString,
				       KmerOccurenceTable * kmerOccurences,
				       Graph * graph,
				       IDnum seqID, Category category,
				       boolean readTracking,
				       boolean double_strand)
{
	Kmer word;
	Kmer antiWord;
	Coordinate readNucleotideIndex;
	Coordinate kmerIndex;
	KmerOccurence *kmerOccurence;
	int wordLength = getWordLength(graph);

	PassageMarker *marker = NULL;
	PassageMarker *previousMarker = NULL;
	Node *node;
	Node *previousNode = NULL;
	Coordinate coord;
	Coordinate previousCoord = 0;
	Nucleotide nucleotide;

	clearKmer(&word);
	clearKmer(&antiWord);

	// Neglect any string shorter than WORDLENGTH :
	if (getLength(tString) < wordLength)
		return;

	// Fill in the initial word : 
	for (readNucleotideIndex = 0;
	     readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
		nucleotide = getNucleotide(readNucleotideIndex, tString);
		pushNucleotide(&word, nucleotide);
		if (double_strand) {
#ifdef COLOR
			reversePushNucleotide(&antiWord, nucleotide);
#else
			reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
		}
	}

	// Go through sequence
	while (readNucleotideIndex < getLength(tString)) {
		nucleotide = getNucleotide(readNucleotideIndex++, tString);
		pushNucleotide(&word, nucleotide);
		if (double_strand) {
#ifdef COLOR
			reversePushNucleotide(&antiWord, nucleotide);
#else
			reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
		}

		// Search in table
		if ((!double_strand || compareKmers(&word, &antiWord) <= 0)
		    && (kmerOccurence =
			findKmerOccurenceInSortedTable(&word,
						       kmerOccurences))) {
			node =
			    getNodeInGraph(graph, kmerOccurence->nodeID);
			coord = kmerOccurence->position;
		} else if ((double_strand && compareKmers(&word, &antiWord) > 0)
			   && (kmerOccurence =
			       findKmerOccurenceInSortedTable(&antiWord,
							      kmerOccurences)))
		{
			node =
			    getNodeInGraph(graph, -kmerOccurence->nodeID);
			coord =
			    getNodeLength(node) - kmerOccurence->position -
			    1;
		} else {
			node = NULL;
			if (previousNode) {
				break;
			}
		}

		// Fill in graph
		if (node) {
			kmerIndex = readNucleotideIndex - wordLength;

			if (previousNode == node
			    && previousCoord == coord - 1) {
				if (category / 2 >= CATEGORIES) {
					setPassageMarkerFinish(marker,
							       kmerIndex +
							       1);
					setFinishOffset(marker,
							getNodeLength(node)
							- coord - 1);
				} else {
					incrementVirtualCoverage(node,
								 category /
								 2, 1);
					incrementOriginalVirtualCoverage
					    (node, category / 2, 1);
				}

			} else {
				if (category / 2 >= CATEGORIES) {
					marker =
					    newPassageMarker(seqID,
							     kmerIndex,
							     kmerIndex + 1,
							     coord,
							     getNodeLength
							     (node) -
							     coord - 1);
					transposePassageMarker(marker,
							       node);
					connectPassageMarkers
					    (previousMarker, marker,
					     graph);
					previousMarker = marker;
				} else {
					if (readTracking) {
						if (!getNodeStatus(node)) {
							addReadStart(node,
								     seqID,
								     coord,
								     graph,
								     kmerIndex);
							setSingleNodeStatus
							    (node, true);
							memorizeNode(node);
						} else {
							blurLastShortReadMarker
							    (node, graph);
						}
					}

					incrementVirtualCoverage(node,
								 category /
								 2, 1);
					incrementOriginalVirtualCoverage
					    (node, category / 2, 1);
				}

				createArc(previousNode, node, graph);
			}

			previousNode = node;
			previousCoord = coord;
		}
	}

	unlockMemorizedNodes();
}