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 projectFromShortRead(Node * node,
ShortReadMarker * shortMarker,
IDnum * readPairs, Category * cats,
ReadOccurence ** readNodes,
IDnum * readNodeCounts,
ShortLength * lengths, boolean weight)
{
IDnum index;
IDnum readIndex = getShortReadMarkerID(shortMarker);
ReadOccurence *readArray;
IDnum readPairIndex;
Category cat;
Coordinate position = getShortReadMarkerPosition(shortMarker);
Coordinate offset = getShortReadMarkerOffset(shortMarker);
Coordinate length = lengths[getShortReadMarkerID(shortMarker) - 1];
Coordinate insertLength;
double insertVariance;
// Filter to remove useless reads
if (position == -1 && offset == -1)
return;
// Going through single-read information
if (readNodeCounts[readIndex] > 1) {
readArray = readNodes[readIndex];
for (index = 0; index < readNodeCounts[readIndex]; index++)
projectFromSingleRead(node, &readArray[index],
position, offset, length,
weight);
}
// Going through paired read information
if (readPairs == NULL)
return;
readPairIndex = readPairs[readIndex - 1] + 1;
if (readPairIndex == 0)
return;
cat = cats[readIndex - 1];
insertLength = getInsertLength(graph, cat);
insertVariance = getInsertLength_var(graph, cat);
readArray = readNodes[readPairIndex];
for (index = 0; index < readNodeCounts[readPairIndex]; index++)
projectFromReadPair(node, &readArray[index], position,
offset, insertLength, insertVariance,
weight);
}
static void projectFromLongRead(Node * node, PassageMarkerI marker,
IDnum * readPairs, Category * cats,
ReadOccurence ** readNodes,
IDnum * readNodeCounts,
ShortLength * lengths, boolean weight)
{
IDnum index;
IDnum readIndex = getPassageMarkerSequenceID(marker);
ReadOccurence *readArray;
IDnum readPairIndex;
Category cat;
Coordinate position = getStartOffset(marker);
Coordinate offset = getPassageMarkerStart(marker);
Coordinate length =
lengths[getPassageMarkerSequenceID(marker) - 1];
Coordinate insertLength;
double insertVariance;
// Going through single-read information
if (readNodeCounts[readIndex] > 1 && position >= 0) {
readArray = readNodes[readIndex];
for (index = 0; index < readNodeCounts[readIndex]; index++)
projectFromSingleRead(node, &readArray[index],
position, offset, length,
weight);
}
// Going through paired read information
if (readPairs == NULL)
return;
readPairIndex = readPairs[readIndex - 1] + 1;
if (readPairIndex == 0)
return;
cat = cats[readIndex - 1];
insertLength = getInsertLength(graph, cat);
insertVariance = getInsertLength_var(graph, cat);
readArray = readNodes[readPairIndex];
for (index = 0; index < readNodeCounts[readPairIndex]; index++)
projectFromReadPair(node, &readArray[index], position,
offset, insertLength, insertVariance,
weight);
}
static IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,
IDnum ** counts, Category cat)
{
Node *A = getNodeInGraph(graph, IDA);
Node *B = connect->destination;
double left, middle, right;
Coordinate longLength, shortLength, D;
IDnum longCount;
double M, N, O, P;
Coordinate mu = getInsertLength(graph, cat);
double sigma = sqrt(getInsertLength_var(graph, cat));
double result;
if (mu <= 0)
return 0;
if (getNodeLength(A) < getNodeLength(B)) {
longLength = getNodeLength(B);
shortLength = getNodeLength(A);
longCount = counts[cat][getNodeID(B) + nodeCount(graph)];
} else {
longLength = getNodeLength(A);
shortLength = getNodeLength(B);
longCount = counts[cat][IDA + nodeCount(graph)];
}
D = connect->distance - (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 = (longCount * (left + middle + right)) / longLength;
if (result > 0)
return (IDnum) result;
else
return 0;
}
