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);
}
}
}
