// Threads each sequences and creates preArcs according to road map indications static void connectPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph, IDnum * chains) { IDnum sequenceIndex; IDnum referenceCount = rdmaps->referenceCount; #ifdef _OPENMP annotationOffset = mallocOrExit(rdmaps->length + 1, Coordinate); annotationOffset[0] = 0; for (sequenceIndex = 1; sequenceIndex <= rdmaps->length; sequenceIndex++) annotationOffset[sequenceIndex] = annotationOffset[sequenceIndex - 1] + getAnnotationCount(getRoadMapInArray(rdmaps, sequenceIndex - 1)); #else Annotation *annot = rdmaps->annotations; #endif if (rdmaps->referenceCount > 0) allocatePreMarkerCountSpace_pg(preGraph); #ifdef _OPENMP int threads = omp_get_max_threads(); if (threads > 8) threads = 8; #pragma omp parallel for num_threads(threads) #endif for (sequenceIndex = 1; sequenceIndex <= sequenceCount_pg(preGraph); sequenceIndex++) { #ifdef _OPENMP Annotation *annot = getAnnotationInArray(rdmaps->annotations, annotationOffset[sequenceIndex - 1]); #endif RoadMap *rdmap; Coordinate currentPosition, currentInternalPosition; IDnum currentPreNodeID, nextInternalPreNodeID; IDnum annotIndex, lastAnnotIndex; boolean isReference; if (sequenceIndex % 1000000 == 0) velvetLog("Connecting %li / %li\n", (long) sequenceIndex, (long) sequenceCount_pg(preGraph)); rdmap = getRoadMapInArray(rdmaps, sequenceIndex - 1); annotIndex = 0; lastAnnotIndex = getAnnotationCount(rdmap); nextInternalPreNodeID = chooseNextInternalPreNode (chains[sequenceIndex] - 1, sequenceIndex, preGraph, chains); isReference = (sequenceIndex <= referenceCount); currentPosition = 0; currentInternalPosition = 0; currentPreNodeID = 0; // Recursion up to last annotation while (annotIndex < lastAnnotIndex || nextInternalPreNodeID != 0) { if (annotIndex == lastAnnotIndex || (nextInternalPreNodeID != 0 && currentInternalPosition < getPosition(annot))) { connectPreNodeToTheNext(¤tPreNodeID, nextInternalPreNodeID, ¤tPosition, sequenceIndex, isReference, preGraph); nextInternalPreNodeID = chooseNextInternalPreNode (currentPreNodeID, sequenceIndex, preGraph, chains); currentInternalPosition += getPreNodeLength_pg(currentPreNodeID, preGraph); } else { connectAnnotation(¤tPreNodeID, annot, ¤tPosition, sequenceIndex, isReference, preGraph); annot = getNextAnnotation(annot); annotIndex++; } } } if (rdmaps->referenceCount > 0) { allocatePreMarkerSpace_pg(preGraph); createPreMarkers(rdmaps, preGraph, chains); } #ifdef _OPENMP free(annotationOffset); annotationOffset = NULL; #endif }
// Threads each sequences and creates preArcs according to road map indications static void connectPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph, IDnum * chains) { Coordinate currentPosition, currentInternalPosition; IDnum sequenceIndex; Annotation *annot = rdmaps->annotations; IDnum referenceCount = rdmaps->referenceCount; IDnum currentPreNodeID, nextInternalPreNodeID; RoadMap *rdmap; IDnum annotIndex, lastAnnotIndex; boolean isReference; if (rdmaps->referenceCount > 0) allocatePreMarkerCountSpace_pg(preGraph); for (sequenceIndex = 1; sequenceIndex <= sequenceCount_pg(preGraph); sequenceIndex++) { if (sequenceIndex % 100000 == 0) velvetLog("Connecting %li / %li\n", (long) sequenceIndex, (long) sequenceCount_pg(preGraph)); rdmap = getRoadMapInArray(rdmaps, sequenceIndex - 1); annotIndex = 0; lastAnnotIndex = getAnnotationCount(rdmap); nextInternalPreNodeID = chooseNextInternalPreNode (chains[sequenceIndex] - 1, sequenceIndex, preGraph, chains); isReference = (sequenceIndex <= referenceCount); currentPosition = 0; currentInternalPosition = 0; currentPreNodeID = 0; // Recursion up to last annotation while (annotIndex < lastAnnotIndex || nextInternalPreNodeID != 0) { if (annotIndex == lastAnnotIndex || (nextInternalPreNodeID != 0 && currentInternalPosition < getPosition(annot))) { connectPreNodeToTheNext(¤tPreNodeID, nextInternalPreNodeID, ¤tPosition, sequenceIndex, isReference, preGraph); nextInternalPreNodeID = chooseNextInternalPreNode (currentPreNodeID, sequenceIndex, preGraph, chains); currentInternalPosition += getPreNodeLength_pg(currentPreNodeID, preGraph); } else { connectAnnotation(¤tPreNodeID, annot, ¤tPosition, sequenceIndex, isReference, preGraph); annot = getNextAnnotation(annot); annotIndex++; } } } if (rdmaps->referenceCount > 0) { allocatePreMarkerSpace_pg(preGraph); createPreMarkers(rdmaps, preGraph, chains); } }