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);
}
//todo: filter chromIndex=ushort.Max
public NsaWriter(ExtendedBinaryWriter writer, ExtendedBinaryWriter indexWriter, DataSourceVersion version, ISequenceProvider refProvider, string jsonKey, bool matchByAllele, bool isArray, int schemaVersion, bool isPositional, bool skipIncorrectRefEntries = true, bool throwErrorOnConflicts = false, int blockSize = SaCommon.DefaultBlockSize)
{
_stream = writer.BaseStream;
_writer = writer;
_isPositional = isPositional;
_skipIncorrectRefEntries = skipIncorrectRefEntries;
_throwErrorOnConflicts = throwErrorOnConflicts;
_block = new NsaBlock(new Zstandard(), blockSize);
_refProvider = refProvider;
_index = new ChunkedIndex(indexWriter, refProvider.Assembly, version, jsonKey, matchByAllele, isArray, schemaVersion, isPositional);
_memBuffer = new byte[short.MaxValue * 2];
_memStream = new MemoryStream(_memBuffer);
_memWriter = new ExtendedBinaryWriter(_memStream);
}
