static boolean pushNeighbours(Node * node, Node * oppositeNode,
Coordinate distance, boolean force_jumps)
{
Node *candidate;
Coordinate oldLength = getNodeLength(node);
MiniConnection *localConnect;
NodeList *path, *tmp;
if ((path = pathIsClear(node, oppositeNode, distance))) {
while (path) {
candidate = path->node;
tmp = path->next;
deallocateNodeList(path);
path = tmp;
///////////////////////////////////////
// Stepping forward to destination //
///////////////////////////////////////
if (getUniqueness(candidate)) {
concatenateReadStarts(node, candidate,
graph);
concatenateLongReads(node, candidate,
graph);
absorbExtension(node, candidate);
// Scaffold changes
recenterNode(node, oldLength);
recenterLocalScaffold(node, oldLength);
absorbExtensionInScaffold(node, candidate);
// Read coverage
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++) {
incrementVirtualCoverage(node, cat,
getVirtualCoverage(candidate, cat));
incrementOriginalVirtualCoverage(node, cat,
getOriginalVirtualCoverage(candidate, cat));
}
#else
incrementVirtualCoverage(node, getVirtualCoverage(candidate));
#endif
if (getNodeStatus(candidate)) {
localConnect =
&localScaffold[getNodeID
(candidate) +
nodeCount
(graph)];
if (localConnect->frontReference) {
destroyConnection
(localConnect->
frontReference,
getNodeID(node));
localConnect->
frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection
(localConnect->
backReference,
-getNodeID(node));
localConnect->
backReference = NULL;
}
unmarkNode(candidate,
localConnect);
}
if (getNodeStatus(getTwinNode(candidate))) {
localConnect =
&localScaffold[-getNodeID
(candidate) +
nodeCount
(graph)];
if (localConnect->frontReference) {
destroyConnection
(localConnect->
frontReference,
getNodeID(node));
localConnect->
frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection
(localConnect->
backReference,
-getNodeID(node));
localConnect->
backReference = NULL;
}
unmarkNode(getTwinNode(candidate),
localConnect);
}
destroyNode(candidate, graph);
return true;
} else {
adjustShortReads(node, candidate);
adjustLongReads(node, getNodeLength(candidate));
absorbExtension(node, candidate);
}
}
}
if (force_jumps && oppositeNode
&& abs_ID(getNodeID(oppositeNode)) < abs_ID(getNodeID(node))) {
distance -= getNodeLength(node) / 2;
distance -= getNodeLength(oppositeNode) / 2;
if (distance > 10) {
adjustShortReadsByLength(node, distance);
adjustLongReads(node, distance);
appendGap(node, distance, graph);
} else {
adjustShortReadsByLength(node, 10);
adjustLongReads(node, 10);
appendGap(node, 10, graph);
}
concatenateReadStarts(node, oppositeNode, graph);
concatenateLongReads(node, oppositeNode, graph);
absorbExtension(node, oppositeNode);
// Scaffold changes
recenterNode(node, oldLength);
recenterLocalScaffold(node, oldLength);
absorbExtensionInScaffold(node, oppositeNode);
// Read coverage
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++)
incrementVirtualCoverage(node, cat,
getVirtualCoverage(oppositeNode, cat));
#else
incrementVirtualCoverage(node, getVirtualCoverage(oppositeNode));
#endif
if (getNodeStatus(oppositeNode)) {
localConnect =
&localScaffold[getNodeID(oppositeNode) +
nodeCount(graph)];
if (localConnect->frontReference) {
destroyConnection(localConnect->
frontReference,
getNodeID(node));
localConnect->frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection(localConnect->
backReference,
-getNodeID(node));
localConnect->backReference = NULL;
}
unmarkNode(oppositeNode, localConnect);
}
if (getNodeStatus(getTwinNode(oppositeNode))) {
localConnect =
&localScaffold[-getNodeID(oppositeNode) +
nodeCount(graph)];
if (localConnect->frontReference) {
destroyConnection(localConnect->
frontReference,
getNodeID(node));
localConnect->frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection(localConnect->
backReference,
-getNodeID(node));
localConnect->backReference = NULL;
}
unmarkNode(getTwinNode(oppositeNode),
localConnect);
}
destroyNode(oppositeNode, graph);
}
return false;
}
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;
}
