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); }
static void comparePaths_local(Node * destination, Node * origin) { IDnum slowLength, fastLength; Node *fastNode, *slowNode; IDnum i; PassageMarkerI marker; //Measure lengths slowLength = fastLength = 0; fastNode = destination; slowNode = origin; //velvetLog("Looking into separate paths\n"); while (fastNode != slowNode) { //velvetLog("Fast node %li Slow node %li\n", getNodeID(fastNode), getNodeID(slowNode)); if (getNodeTime(fastNode) > getNodeTime(slowNode)) { fastLength++; fastNode = getNodePrevious(fastNode); } else if (getNodeTime(fastNode) < getNodeTime(slowNode)) { slowLength++; slowNode = getNodePrevious(slowNode); } else if (isPreviousToNode(slowNode, fastNode)) { while (fastNode != slowNode) { fastLength++; fastNode = getNodePrevious(fastNode); } } else if (isPreviousToNode(fastNode, slowNode)) { while (slowNode != fastNode) { slowLength++; slowNode = getNodePrevious(slowNode); } } else { fastLength++; fastNode = getNodePrevious(fastNode); slowLength++; slowNode = getNodePrevious(slowNode); } if (slowLength > MAXNODELENGTH || fastLength > MAXNODELENGTH) { //velvetLog("Paths too fragmented %li %li\n", slowLength, fastLength); return; } } if (fastLength == 0) return; //Backtracking to record actual paths fastPath = addUncertainPassageMarker(1, destination); setPassageMarkerStatus(fastPath, true); for (i = 0; i < fastLength; i++) { marker = addUncertainPassageMarker(1, getNodePrevious(getNode (fastPath))); setPassageMarkerStatus(marker, true); connectPassageMarkers(marker, fastPath, graph); fastPath = marker; } slowPath = addUncertainPassageMarker(2, destination); setPassageMarkerStatus(slowPath, true); marker = addUncertainPassageMarker(2, origin); setPassageMarkerStatus(marker, true); connectPassageMarkers(marker, slowPath, graph); slowPath = marker; for (i = 0; i < slowLength; i++) { marker = addUncertainPassageMarker(2, getNodePrevious(getNode (slowPath))); setPassageMarkerStatus(marker, true); connectPassageMarkers(marker, slowPath, graph); slowPath = marker; } //Extract sequences if (!extractSequence(fastPath, fastSequence) || !extractSequence(slowPath, slowSequence)) { //velvetLog("Paths too long\n"); destroyPaths(); return; } //Compare sequences if (compareSequences(fastSequence, slowSequence)) { //velvetLog("Correcting discrepancy\n"); cleanUpRedundancy_local(); return; } //velvetLog("\tFinished comparing paths, changes made\n"); destroyPaths(); }
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(); }