public void Query_chunks_in_same_chrom()
{
var stream = new MemoryStream();
var writer = new ExtendedBinaryWriter(stream);
var version = new DataSourceVersion("dbsnp", "150", DateTime.Now.Ticks, "dbsnp ids");
var index = new ChunkedIndex(writer, GenomeAssembly.GRCh37, version, "dbsnp", true, true, SaCommon.SchemaVersion, false);
index.Add(0, 100, 2000, 23457, 89320);
index.Add(0, 2100, 4000, 112778, 58746);
index.Add(0, 4100, 7000, 171525, 658794);
(long start, int chunkCount) = index.GetFileRange(0, 150, 2120);
Assert.Equal(23457, start);
Assert.Equal(2, chunkCount);
(start, chunkCount) = index.GetFileRange(0, 50, 98);
Assert.Equal(-1, start);
Assert.Equal(0, chunkCount);
(start, chunkCount) = index.GetFileRange(0, 150, 2010);
Assert.Equal(23457, start);
Assert.Equal(1, chunkCount);
(start, chunkCount) = index.GetFileRange(0, 2010, 4050);
Assert.Equal(112778, start);
Assert.Equal(1, chunkCount);
(start, chunkCount) = index.GetFileRange(0, 4010, 4050);
Assert.Equal(-1, start);
Assert.Equal(0, chunkCount);
(start, chunkCount) = index.GetFileRange(0, 7010, 7050);
Assert.Equal(-1, start);
Assert.Equal(0, chunkCount);
}
private void Flush(ushort chromIndex)
{
if (_block.BlockOffset == 0)
{
return;
}
long fileOffset = _stream.Position;
(int firstPosition, int lastPosition, int numBytes) = _block.Write(_writer);
_block.Clear();
_index.Add(chromIndex, firstPosition, lastPosition, fileOffset, numBytes);
}