static void concatenateLongReads(Node * node, Node * candidate, Graph * graph) { PassageMarkerI marker, tmpMarker; // Passage marker management in node: for (marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker)) { if (!goesToNode(marker, candidate)) incrementFinishOffset(marker, getNodeLength(candidate)); } // Swapping new born passageMarkers from candidate to node for (marker = getMarker(candidate); marker != NULL_IDX; marker = tmpMarker) { tmpMarker = getNextInNode(marker); if (!comesFromNode(marker, node)) { extractPassageMarker(marker); incrementStartOffset(marker, getNodeLength(node)); transposePassageMarker(marker, node); incrementFinishOffset(getTwinMarker(marker), getNodeLength(node)); } else { reconnectPassageMarker(marker, node, &tmpMarker); } } }
static void updateMembers(Node * bypass, Node * nextNode) { PassageMarkerI marker, next, tmp; Coordinate nextLength = getNodeLength(nextNode); // Update marker + arc info for (marker = getMarker(bypass); marker != NULL_IDX; marker = tmp) { tmp = getNextInNode(marker); if (!isTerminal(marker) && getNode(getNextInSequence(marker)) == nextNode) { // Marker steps right into target next = getNextInSequence(marker); disconnectNextPassageMarker(marker, graph); destroyPassageMarker(next); } else if (getUniqueness(nextNode) && goesToNode(marker, nextNode)) { // Marker goes indirectly to target while (getNode(getNextInSequence(marker)) != nextNode) { next = getNextInSequence(marker); disconnectNextPassageMarker(marker, graph); destroyPassageMarker(next); } next = getNextInSequence(marker); disconnectNextPassageMarker(marker, graph); destroyPassageMarker(next); } else if (!isTerminal(marker) && getFinishOffset(marker) == 0) { // Marker goes somewhere else than to target next = getNextInSequence(marker); incrementFinishOffset(marker, nextLength); } else { // Marker goes nowhere incrementFinishOffset(marker, nextLength); } } }