static void markInterestingNodes(Node * node)
{
Connection *connect;
Node *destination;
MiniConnection *localConnect;
Coordinate min_distance =
getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
// Mark own node
setEmptyMiniConnection(node);
// Loop thru primary scaffold
for (connect = getConnection(node); connect != NULL;
connect = getNextConnection(connect)) {
destination = getTwinNode(getConnectionDestination(connect));
localConnect =
&localScaffold[getNodeID(destination) +
nodeCount(graph)];
if (getNodeStatus(destination)) {
readjustMiniConnection(destination, localConnect,
getConnectionDistance(connect),
min_distance,
getConnectionVariance(connect), connect,
NULL);
localConnect->backReference = NULL;
} else {
resetMiniConnection(destination, localConnect,
getConnectionDistance(connect),
getConnectionVariance(connect), connect,
NULL, true);
}
integrateDerivativeDistances(connect, min_distance, true);
}
// Loop thru twin's primary scaffold
for (connect = getConnection(getTwinNode(node)); connect != NULL;
connect = getNextConnection(connect)) {
destination = getConnectionDestination(connect);
localConnect =
&localScaffold[getNodeID(destination) +
nodeCount(graph)];
if (getNodeStatus(destination))
readjustMiniConnection(destination, localConnect,
-getConnectionDistance(connect),
min_distance,
getConnectionVariance(connect), NULL,
connect);
else
resetMiniConnection(destination, localConnect,
-getConnectionDistance(connect),
getConnectionVariance(connect), NULL,
connect, -1);
integrateDerivativeDistances(connect, min_distance, false);
}
}
void produceTranscript(Locus * locus, IDnum nodesInList)
{
IDnum index = 0;
Node *node;
Transcript *transcript = newTranscript(nodesInList, ((double) nodesInList) / getContigCount(locus));
while ((node = popNodeRecord())) {
transcript->contigs[index] = node;
if (index > 0) {
transcript->distances[index - 1] =
getConnectionDistance((getConnectionBetweenNodes(transcript->contigs[index - 1], getTwinNode(node))));
transcript->distances[index - 1] -=
getNodeLength(node)/2;
transcript->distances[index - 1] -=
getNodeLength(transcript->contigs[index - 1])/2;
if (getNodeLength(node) % 2 > 0 || getNodeLength(transcript->contigs[index - 1]) % 2 > 0)
transcript->distances[index - 1] -= 1;
if (transcript->distances[index - 1] < 0)
transcript->distances[index - 1] = 0;
}
index++;
}
transcript->contigCount = index;
addTranscript(locus, transcript);
}
static IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,
IDnum ** counts, Category cat)
{
Node *A = getNodeInGraph(graph, IDA);
Node *B = connect->destination;
IDnum IDB = getNodeID(B);
double left, middle, right;
Coordinate longLength, shortLength, D;
double M, N, O, P;
Coordinate mu = getInsertLength(graph, cat);
double sigma = sqrt(getInsertLength_var(graph, cat));
double result;
double densityA, densityB, minDensity;
if (mu <= 0)
return 0;
if (getNodeLength(A) == 0 || getNodeLength(B) == 0)
return 0;
if (getNodeLength(A) < getNodeLength(B)) {
longLength = getNodeLength(B);
shortLength = getNodeLength(A);
} else {
longLength = getNodeLength(A);
shortLength = getNodeLength(B);
}
densityA = counts[cat][IDA + nodeCount(graph)] / (double) getNodeLength(A);
densityB = counts[cat][IDB + nodeCount(graph)] / (double) getNodeLength(B);
minDensity = densityA > densityB ? densityB : densityA;
D = getConnectionDistance(connect) - (longLength +
shortLength) / 2;
M = (D - mu) / sigma;
N = (D + shortLength - mu) / sigma;
O = (D + longLength - mu) / sigma;
P = (D + shortLength + longLength - mu) / sigma;
left = ((norm(M) - norm(N)) - M * normInt(M, N)) * sigma;
middle = shortLength * normInt(N, O);
right = ((norm(O) - norm(P)) - P * normInt(O, P)) * (-sigma);
result = (minDensity * (left + middle + right));
if (result > 0)
return (IDnum) result;
else
return 0;
}
static void recenterNode(Node * node, Coordinate oldLength)
{
IDnum nodeID = getNodeID(node);
Connection *connect, *next;
Coordinate distance_shift = (getNodeLength(node) - oldLength) / 2;
Coordinate min_distance =
getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
MiniConnection *localConnect;
//velvetLog("Recentering node\n");
for (connect = getConnection(node); connect != NULL;
connect = next) {
next = getNextConnection(connect);
incrementConnectionDistance(connect, -distance_shift);
if (getConnectionDistance(connect) < min_distance) {
//velvetLog("Unrecording %li\n",
// -getNodeID(getConnectionDestination(connect)));
localConnect =
&localScaffold[-getNodeID(getConnectionDestination(connect))
+ nodeCount(graph)];
localConnect->frontReference = NULL;
unmarkNode(getTwinNode(getConnectionDestination(connect)),
localConnect);
destroyConnection(connect, nodeID);
} else if (getTwinConnection(connect) != NULL)
incrementConnectionDistance(getTwinConnection(connect), -distance_shift);
}
for (connect = getConnection(getTwinNode(node)); connect != NULL;
connect = next) {
next = getNextConnection(connect);
incrementConnectionDistance(connect, distance_shift);
if (getTwinConnection(connect) != NULL)
incrementConnectionDistance(getTwinConnection(connect), distance_shift);
}
}
static void projectFromReadPair(Node * node, ReadOccurence * readOccurence,
Coordinate position, Coordinate offset,
Coordinate insertLength,
double insertVariance, boolean weight)
{
Coordinate distance = insertLength;
Coordinate variance = insertVariance;
Node *target = getNodeInGraph(graph, readOccurence->nodeID);
Connection *connect;
double score;
// Filter for useless reads:
if (readOccurence->position == -1 && readOccurence->offset == -1)
return;
if (target == getTwinNode(node) || target == node)
return;
if (getUniqueness(target) && getNodeID(target) < getNodeID(node))
return;
if (weight) {
if (position > 0 && readOccurence->position > 0
&& (connect =
getConnectionBetweenNodes(node, target))) {
distance = getConnectionDistance(connect);
distance -=
position - offset - getNodeLength(node) / 2;
distance -=
readOccurence->position -
readOccurence->offset -
getNodeLength(target) / 2;
score =
K *
exp((insertLength - distance) * (distance -
insertLength)
/ (2 * insertVariance));
incrementConnectionWeight(connect, score);
}
return;
}
if (position < 0) {
variance += getNodeLength(node) * getNodeLength(node) / 16;
// distance += 0;
} else {
// variance += 0;
distance += position - offset - getNodeLength(node) / 2;
}
if (readOccurence->position < 0) {
variance +=
getNodeLength(target) * getNodeLength(target) / 16;
//distance += 0;
} else {
// variance += 0;
distance +=
readOccurence->position - readOccurence->offset -
getNodeLength(target) / 2;
}
if (distance - getNodeLength(node) / 2 -
getNodeLength(target) / 2 < -6 * sqrt(insertVariance))
return;
createConnection(getNodeID(node), getNodeID(target), 0, 1,
distance, variance);
}
static void absorbExtensionInScaffold(Node * node, Node * source)
{
IDnum nodeID = getNodeID(node);
IDnum sourceID = getNodeID(source);
IDnum sourceIndex = sourceID + nodeCount(graph);
Node *twinSource = getTwinNode(source);
IDnum twinSourceIndex = getNodeID(twinSource) + nodeCount(graph);
Connection *connect, *original;
Node *destination;
IDnum destinationID;
Coordinate distance_shift =
(getNodeLength(node) - getNodeLength(source)) / 2;
Coordinate min_distance =
getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
MiniConnection *localConnect;
Coordinate distance;
double variance;
IDnum direct_count;
IDnum paired_count;
while ((connect = getConnection(source))) {
destination = getTwinNode(getConnectionDestination(connect));
if (destination == getTwinNode(node)) {
localConnect = &localScaffold[twinSourceIndex];
localConnect->frontReference = NULL;
unmarkNode(twinSource, localConnect);
destroyConnection(connect, sourceID);
continue;
}
if (destination == node) {
localConnect = &localScaffold[sourceIndex];
localConnect->backReference = NULL;
unmarkNode(source, localConnect);
destroyConnection(connect, sourceID);
continue;
}
destinationID = getNodeID(destination);
localConnect =
&localScaffold[destinationID + nodeCount(graph)];
incrementConnectionDistance(connect, distance_shift);
distance = getConnectionDistance(connect);
variance = getConnectionVariance(connect);
direct_count = getConnectionDirectCount(connect);
paired_count = getConnectionPairedCount(connect);
if (getNodeStatus(destination)) {
readjustMiniConnection(destination, localConnect,
distance, min_distance,
variance, NULL, NULL);
if ((original = localConnect->frontReference))
readjustConnection(original, distance,
variance, direct_count,
paired_count);
else
localConnect->frontReference =
createNewConnection(nodeID,
-destinationID,
direct_count,
paired_count,
distance,
variance);
} else
resetMiniConnection(destination, localConnect,
distance, variance,
createNewConnection(nodeID,
-destinationID,
direct_count,
paired_count,
distance,
variance),
NULL, true);
integrateDerivativeDistances(connect, min_distance, true);
destroyConnection(connect, sourceID);
}
// Loop thru twin's primary scaffold
while ((connect = getConnection(getTwinNode(source)))) {
destination = getConnectionDestination(connect);
if (destination == node) {
localConnect = &localScaffold[sourceIndex];
localConnect->frontReference = NULL;
unmarkNode(source, localConnect);
destroyConnection(connect, -sourceID);
continue;
}
if (destination == getTwinNode(node)) {
localConnect = &localScaffold[twinSourceIndex];
localConnect->backReference = NULL;
unmarkNode(twinSource, localConnect);
destroyConnection(connect, -sourceID);
continue;
}
destinationID = getNodeID(destination);
localConnect =
&localScaffold[destinationID + nodeCount(graph)];
incrementConnectionDistance(connect, -distance_shift);
distance = getConnectionDistance(connect);
variance = getConnectionVariance(connect);
direct_count = getConnectionDirectCount(connect);
paired_count = getConnectionPairedCount(connect);
if (distance > min_distance && getNodeStatus(destination) < 0) {
readjustMiniConnection(destination, localConnect,
-distance, min_distance,
variance, NULL, NULL);
if ((original = localConnect->backReference))
readjustConnection(original, distance,
variance, direct_count,
paired_count);
} else if (getNodeStatus(destination) < 0) {
if ((original = localConnect->backReference)) {
destroyConnection(original, -nodeID);
localConnect->backReference = NULL;
}
unmarkNode(destination, localConnect);
} else if (getNodeStatus(destination) > 0) {
if ((original = localConnect->frontReference)) {
destroyConnection(original, nodeID);
localConnect->frontReference = NULL;
}
unmarkNode(destination, localConnect);
} else if (distance > min_distance) {
resetMiniConnection(destination, localConnect,
-distance, variance, NULL,
createNewConnection(-nodeID,
destinationID,
direct_count,
paired_count,
distance,
variance),
-1);
integrateDerivativeDistances(connect, min_distance, true);
}
destroyConnection(connect, -sourceID);
}
}
static void integrateDerivativeDistances(Connection * connect,
Coordinate min_distance,
boolean direction)
{
Node *reference = getConnectionDestination(connect);
Node *destination;
IDnum destinationID;
Coordinate distance, baseDistance;
double variance, baseVariance;
Connection *connect2;
MiniConnection *localConnect;
// debug
IDnum counter = 0;
if (!getUniqueness(reference))
return;
//velvetLog("Opposite node %li length %li at %li ± %f\n", getNodeID(reference), getNodeLength(reference), getConnectionDistance(connect), getConnectionVariance(connect));
baseDistance = getConnectionDistance(connect);
baseVariance = getConnectionVariance(connect);
for (connect2 = getConnection(reference);
connect2 != NULL; connect2 = getNextConnection(connect2)) {
// Avoid null derivative
if (connect2 == getTwinConnection(connect))
continue;
destination = getConnectionDestination(connect2);
// Beware of directionality
if (!direction)
destination = getTwinNode(destination);
// Derivate values
destinationID = getNodeID(destination);
// Beware of directionality (bis)
if (direction)
distance = baseDistance - getConnectionDistance(connect2);
else
distance = getConnectionDistance(connect2) - baseDistance;
variance = getConnectionVariance(connect2) + baseVariance;
localConnect =
&localScaffold[destinationID + nodeCount(graph)];
// Avoid over-projection
if (distance < min_distance) {
//velvetLog("Node %li not at distance %li± %f (min %li)\n", destinationID, distance, variance, min_distance);
continue;
}
counter++;
if (getNodeStatus(destination)) {
readjustMiniConnection(destination, localConnect,
distance, min_distance,
variance, NULL, NULL);
} else
resetMiniConnection(destination, localConnect,
distance, variance, NULL, NULL,
true);
//velvetLog("Node %li now at distance %li\n", destinationID, localConnect->distance);
}
//velvetLog("%li secondary distances added\n", counter);
}
