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 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);
}
}
}
