static boolean * countCoOccurences(IDnum * coOccurencesCount, ReadOccurence ** readNodes, IDnum * readNodeCounts, IDnum * readPairs, Category * cats) {
IDnum readIndex, readPairIndex;
IDnum readNodeCount;
IDnum readOccurenceIndex, readPairOccurenceIndex;
ReadOccurence * readOccurence, *readPairOccurence;
boolean * interestingReads = callocOrExit(sequenceCount(graph), boolean);
Category libID;
for (libID = 0; libID < CATEGORIES + 1; libID++)
coOccurencesCount[libID] = 0;
for (readIndex = 0; readIndex < sequenceCount(graph); readIndex++) {
// Eliminating dodgy, unpaired, already counted or user-specified reads
if ( readPairs[readIndex] < readIndex
|| getInsertLength(graph, cats[readIndex]) > -1)
continue;
// Check for co-occurence
// We know that for each read the read occurences are ordered by increasing node ID
// Therefore one list is followed by increasing index, whereas the other is followed
// by decreasing index
libID = cats[readIndex]/2;
readPairIndex = readPairs[readIndex];
readOccurenceIndex = 0;
readOccurence = readNodes[readIndex + 1];
readNodeCount = readNodeCounts[readIndex + 1];
readPairOccurenceIndex = readNodeCounts[readPairIndex + 1] - 1;
readPairOccurence = &(readNodes[readPairIndex + 1][readPairOccurenceIndex]);
while (readOccurenceIndex < readNodeCount && readPairOccurenceIndex >= 0) {
if (readOccurence->nodeID == -readPairOccurence->nodeID) {
if (readOccurence->position > 0 && readPairOccurence->position > 0) {
coOccurencesCount[libID]++;
interestingReads[readIndex] = true;
break;
} else {
readOccurence++;
readOccurenceIndex++;
readPairOccurence--;
readPairOccurenceIndex--;
}
} else if (readOccurence->nodeID < -readPairOccurence->nodeID) {
readOccurence++;
readOccurenceIndex++;
} else {
readPairOccurence--;
readPairOccurenceIndex--;
}
}
}
return interestingReads;
}
static IDnum *computeReadToNodeCounts()
{
IDnum readIndex, nodeIndex;
IDnum maxNodeIndex = 2 * nodeCount(graph) + 1;
IDnum maxReadIndex = sequenceCount(graph) + 1;
IDnum *readNodeCounts = callocOrExit(maxReadIndex, IDnum);
boolean *readMarker = callocOrExit(maxReadIndex, boolean);
ShortReadMarker *nodeArray, *shortMarker;
PassageMarkerI marker;
Node *node;
IDnum nodeReadCount;
//puts("Computing read to node mapping array sizes");
for (nodeIndex = 0; nodeIndex < maxNodeIndex; nodeIndex++) {
node = getNodeInGraph(graph, nodeIndex - nodeCount(graph));
if (node == NULL)
continue;
// Short reads
if (readStartsAreActivated(graph)) {
nodeArray = getNodeReads(node, graph);
nodeReadCount = getNodeReadCount(node, graph);
for (readIndex = 0; readIndex < nodeReadCount; readIndex++) {
shortMarker =
getShortReadMarkerAtIndex(nodeArray,
readIndex);
readNodeCounts[getShortReadMarkerID
(shortMarker)]++;
}
}
// Long reads
for (marker = getMarker(node); marker != NULL_IDX;
marker = getNextInNode(marker)) {
readIndex = getPassageMarkerSequenceID(marker);
if (readIndex < 0)
continue;
if (readMarker[readIndex])
continue;
readNodeCounts[readIndex]++;
readMarker[readIndex] = true;
}
// Clean up marker array
for (marker = getMarker(node); marker != NULL_IDX;
marker = getNextInNode(marker)) {
readIndex = getPassageMarkerSequenceID(marker);
if (readIndex > 0)
readMarker[readIndex] = false;
}
}
free(readMarker);
return readNodeCounts;
}
static void measureCoOccurences(Coordinate ** coOccurences, boolean * interestingReads, ReadOccurence ** readNodes, IDnum * readNodeCounts, IDnum * readPairs, Category * cats) {
IDnum coOccurencesIndex[CATEGORIES + 1];
IDnum observationIndex;
IDnum readIndex, readPairIndex;
IDnum readNodeCount;
IDnum readOccurenceIndex, readPairOccurenceIndex;
ReadOccurence * readOccurence, *readPairOccurence;
Category libID;
for (libID = 0; libID < CATEGORIES + 1; libID++)
coOccurencesIndex[libID] = 0;
for (readIndex = 0; readIndex < sequenceCount(graph); readIndex++) {
// Eliminating dodgy, unpaired, already counted or user-specified reads
if (!interestingReads[readIndex])
continue;
// Find co-occurence
// We know that for each read the read occurences are ordered by increasing node ID
libID = cats[readIndex]/2;
readPairIndex = readPairs[readIndex];
observationIndex = coOccurencesIndex[libID];
readOccurence = readNodes[readIndex + 1];
readOccurenceIndex = 0;
readNodeCount = readNodeCounts[readIndex + 1];
readPairOccurenceIndex = readNodeCounts[readPairIndex + 1] - 1;
readPairOccurence = &(readNodes[readPairIndex + 1][readPairOccurenceIndex]);
while (readOccurenceIndex < readNodeCount && readPairOccurenceIndex >= 0) {
if (readOccurence->nodeID == -readPairOccurence->nodeID) {
if (readOccurence->position > 0 && readPairOccurence->position > 0) {
coOccurences[libID][observationIndex] =
getNodeLength(getNodeInGraph(graph, readOccurence->nodeID))
+ getWordLength(graph) - 1
- (readOccurence->position - readOccurence->offset)
- (readPairOccurence->position - readPairOccurence->offset);
coOccurencesIndex[libID]++;
break;
} else {
readOccurence++;
readOccurenceIndex++;
readPairOccurence--;
readPairOccurenceIndex--;
}
} else if (readOccurence->nodeID < -readPairOccurence->nodeID) {
readOccurence++;
readOccurenceIndex++;
} else {
readPairOccurence--;
readPairOccurenceIndex--;
}
}
}
}
