static void absorbExtension(Node * node, Node * extension)
{
Arc *arc;
appendNodeGaps(node, extension, graph);
appendDescriptors(node, extension);
// Destroy old nodes
while (getArc(node) != NULL)
destroyArc(getArc(node), graph);
// Create new
for (arc = getArc(extension); arc != NULL; arc = getNextArc(arc))
createAnalogousArc(node, getDestination(arc), arc, graph);
}
// Replaces two consecutive nodes into a single equivalent node
// The extra memory is freed
void concatenateNodes(Node * nodeA, Node * nodeB, Graph * graph)
{
PassageMarkerI marker, tmpMarker;
Node *twinA = getTwinNode(nodeA);
Node *twinB = getTwinNode(nodeB);
Arc *arc;
Category cat;
// Arc management:
// Freeing useless arcs
while (getArc(nodeA) != NULL)
destroyArc(getArc(nodeA), graph);
// Correct arcs
for (arc = getArc(nodeB); arc != NULL; arc = getNextArc(arc)) {
if (getDestination(arc) != twinB)
createAnalogousArc(nodeA, getDestination(arc),
arc, graph);
else
createAnalogousArc(nodeA, twinA, arc, graph);
}
// Passage marker management in node A:
for (marker = getMarker(nodeA); marker != NULL_IDX;
marker = getNextInNode(marker))
if (isTerminal(marker))
incrementFinishOffset(marker,
getNodeLength(nodeB));
// Swapping new born passageMarkers from B to A
for (marker = getMarker(nodeB); marker != NULL_IDX; marker = tmpMarker) {
tmpMarker = getNextInNode(marker);
if (isInitial(marker)
|| getNode(getPreviousInSequence(marker)) != nodeA) {
extractPassageMarker(marker);
transposePassageMarker(marker, nodeA);
incrementFinishOffset(getTwinMarker(marker),
getNodeLength(nodeA));
} else
disconnectNextPassageMarker(getPreviousInSequence
(marker), graph);
}
// Read starts
concatenateReadStarts(nodeA, nodeB, graph);
// Gaps
appendNodeGaps(nodeA, nodeB, graph);
// Descriptor management (node)
appendDescriptors(nodeA, nodeB);
// Update uniqueness:
setUniqueness(nodeA, getUniqueness(nodeA) || getUniqueness(nodeB));
// Update virtual coverage
for (cat = 0; cat < CATEGORIES; cat++)
incrementVirtualCoverage(nodeA, cat,
getVirtualCoverage(nodeB, cat));
// Update original virtual coverage
for (cat = 0; cat < CATEGORIES; cat++)
incrementOriginalVirtualCoverage(nodeA, cat,
getOriginalVirtualCoverage
(nodeB, cat));
// Freeing gobbled node
destroyNode(nodeB, graph);
}
static Node *bypass()
{
Node *bypass = getNode(path);
Node *next = NULL;
Arc *arc;
PassageMarkerI nextMarker;
// Remove unwanted arcs
while (getArc(bypass) != NULL)
destroyArc(getArc(bypass), graph);
// Update extensive variables (length + descriptors + passage markers)
while (!isTerminal(path)) {
nextMarker = getNextInSequence(path);
next = getNode(nextMarker);
while (next == bypass) {
disconnectNextPassageMarker(path, graph);
destroyPassageMarker(nextMarker);
nextMarker = getNextInSequence(path);
next = getNode(nextMarker);
}
if (next == NULL)
return bypass;
// Overall node update
if (!getUniqueness(next)) {
adjustShortReads(bypass, getNextInSequence(path));
appendSequence(bypass, sequences,
getNextInSequence(path), graph);
} else {
concatenateReadStarts(bypass, next, graph);
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++) {
// Update virtual coverage
incrementVirtualCoverage(bypass, cat,
getVirtualCoverage(next, cat));
// Update original virtual coverage
incrementOriginalVirtualCoverage(bypass, cat,
getOriginalVirtualCoverage(next, cat));
}
#else
incrementVirtualCoverage(bypass, getVirtualCoverage(next));
#endif
appendDescriptors(bypass, next);
}
// Members
updateMembers(bypass, next);
// Termination
if (isTerminal(path) || getUniqueness(next))
break;
}
// Remove unique groupies from arrival
admitGroupies(next, bypass);
// Copy destination arcs
for (arc = getArc(next); arc != NULL; arc = getNextArc(arc)) {
if (getDestination(arc) == next)
continue;
else if (getDestination(arc) == getTwinNode(next))
createAnalogousArc(bypass, getTwinNode(bypass),
arc, graph);
else
createAnalogousArc(bypass, getDestination(arc),
arc, graph);
}
destroyNode(next, graph);
return bypass;
}
