private static void WriteToPosition(ISaItemTsvWriter writer, MinHeap <SupplementaryDataItem> itemsHeap, int position)
{
if (itemsHeap.Count() == 0)
{
return;
}
var bufferMin = itemsHeap.GetMin();
while (bufferMin.Start < position)
{
var itemsAtMinPosition = new List <SupplementaryDataItem>();
while (itemsHeap.Count() > 0 && bufferMin.CompareTo(itemsHeap.GetMin()) == 0)
{
itemsAtMinPosition.Add(itemsHeap.ExtractMin());
}
writer.WritePosition(itemsAtMinPosition);
if (itemsHeap.Count() == 0)
{
break;
}
bufferMin = itemsHeap.GetMin();
}
}
public static void WriteSortedItems(IEnumerable <SupplementaryDataItem> saItems, ISaItemTsvWriter writer)
{
var itemsMinHeap = new MinHeap <SupplementaryDataItem>();
var currentRefIndex = int.MaxValue;
var benchmark = new Benchmark();
foreach (var saItem in saItems)
{
if (currentRefIndex != saItem.Chromosome.Index)
{
if (currentRefIndex != int.MaxValue)
{
//flushing out the remaining items in buffer
WriteToPosition(writer, itemsMinHeap, int.MaxValue);
//Console.WriteLine($"Wrote out chr{currentRefIndex} items in {benchmark.GetElapsedTime()}");
benchmark.Reset();
}
currentRefIndex = saItem.Chromosome.Index;
//Console.WriteLine("Writing items from chromosome:" + currentRefIndex);
}
//the items come in sorted order of the pre-trimmed position.
//So when writing out, we have to make sure that we do not write past this position.
//Once a position has been seen in the stream, we can safely write all positions before that.
var writeToPos = saItem.Start;
saItem.Trim();
itemsMinHeap.Add(saItem);
WriteToPosition(writer, itemsMinHeap, writeToPos);
}
//flushing out the remaining items in buffer
WriteToPosition(writer, itemsMinHeap, int.MaxValue);
}
