static void computePartialReadToNodeMapping(IDnum nodeID,
ReadOccurence ** readNodes,
IDnum * readNodeCounts,
boolean * readMarker,
ReadSet * reads)
{
ShortReadMarker *shortMarker;
IDnum index, readIndex;
ReadOccurence *readArray, *readOccurence;
Node *node = getNodeInGraph(graph, nodeID);
ShortReadMarker *nodeArray = getNodeReads(node, graph);
IDnum nodeReadCount = getNodeReadCount(node, graph);
PassageMarkerI marker;
for (index = 0; index < nodeReadCount; index++) {
shortMarker = getShortReadMarkerAtIndex(nodeArray, index);
readIndex = getShortReadMarkerID(shortMarker);
readArray = readNodes[readIndex];
readOccurence = &readArray[readNodeCounts[readIndex]];
readOccurence->nodeID = nodeID;
readOccurence->position =
getShortReadMarkerPosition(shortMarker);
readOccurence->offset =
getShortReadMarkerOffset(shortMarker);
readNodeCounts[readIndex]++;
}
for (marker = getMarker(node); marker != NULL_IDX;
marker = getNextInNode(marker)) {
readIndex = getPassageMarkerSequenceID(marker);
if (readIndex <= 0 || reads->categories[readIndex - 1] == REFERENCE)
continue;
if (!readMarker[readIndex]) {
readArray = readNodes[readIndex];
readOccurence =
&readArray[readNodeCounts[readIndex]];
readOccurence->nodeID = nodeID;
readOccurence->position = getStartOffset(marker);
readOccurence->offset =
getPassageMarkerStart(marker);
readNodeCounts[readIndex]++;
readMarker[readIndex] = true;
} else {
readArray = readNodes[readIndex];
readOccurence =
&readArray[readNodeCounts[readIndex] - 1];
readOccurence->position = -1;
readOccurence->offset = -1;
}
}
for (marker = getMarker(node); marker != NULL_IDX;
marker = getNextInNode(marker)) {
readIndex = getPassageMarkerSequenceID(marker);
if (readIndex > 0)
readMarker[readIndex] = false;
}
}
void concatenateReadStarts(Node * target, Node * source, Graph * graph)
{
IDnum sourceLength, targetLength;
ShortReadMarker *sourceArray, *targetArray, *marker;
IDnum index;
Coordinate position, nodeLength;
if (!readStartsAreActivated(graph))
return;
if (target == NULL || source == NULL)
return;
// Update Coordinates
sourceArray = getNodeReads(source, graph);
sourceLength = getNodeReadCount(source, graph);
nodeLength = getNodeLength(target);
for (index = 0; index < sourceLength; index++) {
marker = getShortReadMarkerAtIndex(sourceArray, index);
position = getShortReadMarkerPosition(marker);
if (position != -1) {
position += nodeLength;
setShortReadMarkerPosition(marker, position);
}
}
// Same but for symmetrical reads
targetArray = getNodeReads(getTwinNode(target), graph);
targetLength = getNodeReadCount(getTwinNode(target), graph);
nodeLength = getNodeLength(source);
for (index = 0; index < targetLength; index++) {
marker = getShortReadMarkerAtIndex(targetArray, index);
position = getShortReadMarkerPosition(marker);
if (position != -1) {
position += nodeLength;
setShortReadMarkerPosition(marker, position);
}
}
// Merging lists
mergeNodeReads(target, source, graph);
mergeNodeReads(getTwinNode(target), getTwinNode(source), graph);
}
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 adjustShortReadsByLength(Node * target, Coordinate nodeLength)
{
ShortReadMarker *targetArray, *marker;
IDnum targetLength, index;
Coordinate position;
if (!readStartsAreActivated(graph))
return;
targetArray = getNodeReads(getTwinNode(target), graph);
targetLength = getNodeReadCount(getTwinNode(target), graph);
for (index = 0; index < targetLength; index++) {
marker = getShortReadMarkerAtIndex(targetArray, index);
position = getShortReadMarkerPosition(marker);
if (position != -1) {
position += nodeLength;
setShortReadMarkerPosition(marker, position);
}
}
}
