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 Preload()
{
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description");
using (var saStream = new MemoryStream())
using (var indexStream = new MemoryStream())
{
using (var extWriter = new ExtendedBinaryWriter(saStream, Encoding.UTF8, true))
using (var indexExtWriter = new ExtendedBinaryWriter(indexStream, Encoding.UTF8, true))
{
var saWriter = new NsaWriter(extWriter, indexExtWriter, version, GetAllASequenceProvider(), "dbsnp", true, true, SaCommon.SchemaVersion, false, true, false, 1024);
saWriter.Write(GetDbsnpItems(1000));
}
saStream.Position = 0;
indexStream.Position = 0;
using (var saReader = new NsaReader(saStream, indexStream, 1024))
{
saReader.PreLoad(_chrom1, GetPositions(50, 1000));
Assert.Null(saReader.GetAnnotation(90)); //before any SA existed
Assert.NotNull(saReader.GetAnnotation(100)); //first entry of first block
Assert.NotNull(saReader.GetAnnotation(480)); //last query of first block
Assert.Null(saReader.GetAnnotation(488)); //between first and second block
Assert.NotNull(saReader.GetAnnotation(490)); //first entry of second block
}
}
}
public void Write_clinvar_basic()
{
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description");
using (var saStream = new MemoryStream())
using (var indexStream = new MemoryStream())
{
using (var saWriter = new NsaWriter(saStream, indexStream, version, GetSequenceProvider(), "clinvar",
false, true, SaCommon.SchemaVersion, false, true, false, 1024, GenomeAssembly.GRCh37, true))
{
saWriter.Write(GetClinvarItems());
}
saStream.Position = 0;
indexStream.Position = 0;
using (var saReader = new NsaReader(saStream, indexStream, 1024))
{
Assert.Equal(GenomeAssembly.GRCh37, saReader.Assembly);
Assert.Equal(version.ToString(), saReader.Version.ToString());
saReader.PreLoad(ChromosomeUtilities.Chr1, new List <int> {
100, 101, 106
});
var annotations = saReader.GetAnnotation(100).ToList();
Assert.Equal("T", annotations[0].refAllele);
Assert.Equal("A", annotations[0].altAllele);
Assert.Equal(
"\"id\":\"RCV0001\",\"reviewStatus\":\"no assertion provided\",\"alleleOrigins\":[\"origin1\"],\"refAllele\":\"T\",\"altAllele\":\"A\",\"phenotypes\":[\"phenotype1\"],\"medGenIds\":[\"medgen1\"],\"omimIds\":[\"omim1\"],\"orphanetIds\":[\"orpha1\"],\"significance\":[\"significance\"],\"lastUpdatedDate\":\"0001-01-01\",\"pubMedIds\":[\"10024875684920\"]",
annotations[0].annotation);
annotations = saReader.GetAnnotation(101).ToList();
Assert.Equal("A", annotations[0].refAllele);
Assert.Equal("", annotations[0].altAllele);
Assert.Equal(
"\"id\":\"RCV00011\",\"variationId\":101,\"reviewStatus\":\"no assertion provided\",\"alleleOrigins\":[\"origin1\"],\"refAllele\":\"A\",\"altAllele\":\"-\",\"phenotypes\":[\"phenotype1\"],\"medGenIds\":[\"medgen1\"],\"omimIds\":[\"omim1\"],\"orphanetIds\":[\"orpha1\"],\"significance\":[\"significance\"],\"lastUpdatedDate\":\"0001-01-01\",\"pubMedIds\":[\"10024875684920\"]",
annotations[0].annotation);
saReader.PreLoad(ChromosomeUtilities.Chr2, new List <int> {
200, 205
});
var(refAllele, altAllele, annotation) = saReader.GetAnnotation(200).First();
Assert.Equal("G", refAllele);
Assert.Equal("A", altAllele);
Assert.NotNull(annotation);
}
}
}
