static void identifyUniqueNodes(boolean(*isUniqueFunction) (Node *))
{
IDnum index;
Node *node;
IDnum counter = 0;
velvetLog("Identifying unique nodes\n");
for (index = 1; index <= nodeCount(graph); index++) {
node = getNodeInGraph(graph, index);
if (node == NULL)
continue;
setUniqueness(node, isUniqueFunction(node));
if (getUniqueness(node))
counter++;
}
velvetLog("Done, %li unique nodes counted\n", (long) counter);
}
// 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);
}
// Replaces two consecutive nodes into a single equivalent node
// The extra memory is freed
void concatenateStringOfNodes(Node * nodeA, Graph * graph)
{
Node *twinA = getTwinNode(nodeA);
Node * nodeB = nodeA;
Node * twinB;
Node *currentNode, *nextNode;
Coordinate totalLength = 0;
PassageMarkerI marker, tmpMarker;
Arc *arc;
Category cat;
while (simpleArcCount(nodeB) == 1
&&
simpleArcCount(getTwinNode
(getDestination(getArc(nodeB)))) ==
1
&& getDestination(getArc(nodeB)) != getTwinNode(nodeB)
&& getDestination(getArc(nodeB)) != nodeA) {
totalLength += getNodeLength(nodeB);
nodeB = getDestination(getArc(nodeB));
}
twinB = getTwinNode(nodeB);
totalLength += getNodeLength(nodeB);
reallocateNodeDescriptor(nodeA, totalLength);
currentNode = nodeA;
while (currentNode != nodeB) {
currentNode = getDestination(getArc(currentNode));
// Passage marker management in node A:
for (marker = getMarker(nodeA); marker != NULL_IDX;
marker = getNextInNode(marker))
if (getNode(getNextInSequence(marker)) != currentNode)
incrementFinishOffset(marker,
getNodeLength(currentNode));
// Swapping new born passageMarkers from B to A
for (marker = getMarker(currentNode); 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, currentNode, graph);
// Gaps
appendNodeGaps(nodeA, currentNode, graph);
// Update uniqueness:
setUniqueness(nodeA, getUniqueness(nodeA) || getUniqueness(currentNode));
// Update virtual coverage
for (cat = 0; cat < CATEGORIES; cat++)
incrementVirtualCoverage(nodeA, cat,
getVirtualCoverage(currentNode, cat));
// Update original virtual coverage
for (cat = 0; cat < CATEGORIES; cat++)
incrementOriginalVirtualCoverage(nodeA, cat,
getOriginalVirtualCoverage
(currentNode, cat));
// Descriptor management (node)
directlyAppendDescriptors(nodeA, currentNode, totalLength);
}
// 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);
}
// Freeing gobbled nodes
currentNode = getTwinNode(nodeB);
while (currentNode != getTwinNode(nodeA)) {
arc = getArc(currentNode);
nextNode = getDestination(arc);
destroyNode(currentNode, graph);
currentNode = nextNode;
}
}
static boolean uniqueNodesConnect(Node * startingNode)
{
Node *destination = NULL;
PassageMarkerI startMarker, currentMarker;
RBConnection *newList;
RBConnection *list = NULL;
boolean multipleHits = false;
if (arcCount(startingNode) == 0)
return false;
if (getMarker(startingNode) == NULL_IDX)
return false;
dbgCounter++;
// Checking for multiple destinations
for (startMarker = getMarker(startingNode); startMarker != NULL_IDX;
startMarker = getNextInNode(startMarker)) {
if (getFinishOffset(startMarker) >
2 * getWordLength(graph))
continue;
for (currentMarker = getNextInSequence(startMarker);
currentMarker != NULL_IDX;
currentMarker = getNextInSequence(currentMarker)) {
if (!getUniqueness(getNode(currentMarker))) {
continue;
} else if (getNodeStatus(getNode(currentMarker))) {
if (getStartOffset(currentMarker) >
2 * getWordLength(graph))
break;
for (newList = list; newList != NULL;
newList = newList->next) {
if (newList->node ==
getNode(currentMarker)) {
newList->multiplicity++;
break;
}
}
if (newList == NULL)
abort();
break;
} else {
if (getStartOffset(currentMarker) >
2 * getWordLength(graph))
break;
setSingleNodeStatus(getNode(currentMarker),
true);
newList = allocateRBConnection();
newList->node = getNode(currentMarker);
newList->multiplicity = 1;
newList->marker = startMarker;
newList->next = list;
list = newList;
break;
}
}
}
while (list != NULL) {
newList = list;
list = newList->next;
setSingleNodeStatus(newList->node, false);
if (newList->multiplicity >= MULTIPLICITY_CUTOFF) {
if (destination == NULL) {
destination = newList->node;
path = newList->marker;
} else if (destination != newList->node)
multipleHits = true;
}
deallocateRBConnection(newList);
}
if (multipleHits) {
multCounter++;
setUniqueness(startingNode, false);
return false;
}
if (destination == NULL || destination == startingNode
|| destination == getTwinNode(startingNode)) {
nullCounter++;
return false;
}
// Check for reciprocity
for (startMarker = getMarker(getTwinNode(destination));
startMarker != NULL_IDX;
startMarker = getNextInNode(startMarker)) {
if (getFinishOffset(startMarker) >
2 * getWordLength(graph))
continue;
for (currentMarker = getNextInSequence(startMarker);
currentMarker != NULL_IDX;
currentMarker = getNextInSequence(currentMarker)) {
if (!getUniqueness(getNode(currentMarker))) {
continue;
} else if (getNodeStatus(getNode(currentMarker))) {
if (getStartOffset(currentMarker) >
2 * getWordLength(graph))
break;
for (newList = list; newList != NULL;
newList = newList->next) {
if (newList->node ==
getNode(currentMarker)) {
newList->multiplicity++;
break;
}
}
if (newList == NULL)
abort();
break;
} else {
if (getStartOffset(currentMarker) >
2 * getWordLength(graph))
break;
setSingleNodeStatus(getNode(currentMarker),
true);
newList = allocateRBConnection();
newList->node = getNode(currentMarker);
newList->multiplicity = 1;
newList->next = list;
list = newList;
break;
}
}
}
while (list != NULL) {
newList = list;
list = newList->next;
setSingleNodeStatus(newList->node, false);
if (newList->multiplicity >= MULTIPLICITY_CUTOFF
&& newList->node != getTwinNode(startingNode))
multipleHits = true;
deallocateRBConnection(newList);
}
if (multipleHits) {
multCounter++;
setUniqueness(destination, false);
return false;
}
// Aligning long reads to each other:
// TODO
// Merge pairwise alignments and produce consensus
// TODO
return true;
}
