internal void Write(ushort chromIndex, NsaReader nsaReader)
{
if (nsaReader == null)
{
return;
}
var dataBlocks = nsaReader.GetCompressedBlocks(chromIndex);
var indexBlocks = nsaReader.GetIndexBlocks(chromIndex);
var i = 0;//index of the index Blocks
//cannot convert the dataBlocks into a list since that may take up GBs of memory (proportional to the nas file size)
foreach (var dataBlock in dataBlocks)
{
if (i > indexBlocks.Count)
{
throw new IndexOutOfRangeException("Nsa Index have less blocks than the Nsa file. They have to be the same.");
}
var oldIndexBlock = indexBlocks[i];
_index.Add(chromIndex, oldIndexBlock.Start, oldIndexBlock.End, _writer.BaseStream.Position, oldIndexBlock.Length);
dataBlock.WriteCompressedBytes(_writer);
i++;
}
if (i < indexBlocks.Count)
{
throw new IndexOutOfRangeException("Nsa Index have more blocks than the Nsa file. They have to be the same.");
}
}
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 NsaIndex(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);
}