private JasixNode FindFirstOverlappingNode(JasixNode searchNode)
{
var index = _nodes.BinarySearch(searchNode);
if (index < 0)
{
index = ~index;
}
// if it is to the left of the first node, check if the end overlaps
if (index == 0)
{
return(_nodes[index].Overlaps(searchNode) ? _nodes[index] : null);
}
if (index == _nodes.Count)
{
// if range overlaps the last node location of the last node, otherwise, -1
return(_nodes[index - 1].Overlaps(searchNode) ? _nodes[index - 1] : null);
}
// if some intervals from the previous node overlaps the range
if (_nodes[index - 1].Overlaps(searchNode))
{
return(_nodes[index - 1]);
}
return(_nodes[index].Overlaps(searchNode) ? _nodes[index] : null);
}
public void Add(int begin, int end, long filePosition)
{
if (begin > end)
{
throw new UserErrorException($"start position {begin} is greater than end position{end}");
}
if (Utilities.IsLargeVariant(begin, end))
{
_largeVariants.Add(new Interval <long>(begin, end, filePosition));
end = begin;// large variants will be recorded as snvs so that we can query for all entries from a given position
}
if (_currentNode == null)
{
_currentNode = new JasixNode(begin, end, filePosition);
return;
}
if (_currentNode.TryAdd(begin, end))
{
return;
}
_nodes.Add(_currentNode);
_currentNode = new JasixNode(begin, end, filePosition);
}
public long FindFirstSmallVariant(int start, int end)
{
var searchNode = new JasixNode(start, end, 0);
var firstOverlappingNode = FindFirstOverlappingNode(searchNode);
return(firstOverlappingNode?.FileLocation ?? -1);
}