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);
}
private static ExitCodes ProgramExecution()
{
using (var indexStream = FileUtilities.GetReadStream(_inputIndexFile))
using (var outStream = FileUtilities.GetCreateStream(_outputIndexFile))
using (var extWriter = new ExtendedBinaryWriter(outStream))
{
var version = DataSourceVersionReader.GetSourceVersion(_versionFile);
var oldIndex = new NsaIndex(indexStream);
var newIndex = new NsaIndex(extWriter, oldIndex.Assembly, version, oldIndex.JsonKey, oldIndex.MatchByAllele, oldIndex.IsArray, oldIndex.SchemaVersion, oldIndex.IsPositional);
newIndex.Write(oldIndex.GetBlocks());
}
return(ExitCodes.Success);
}
//todo: filter chromIndex=ushort.Max
public NsaWriter(Stream nsaStream, Stream indexStream, IDataSourceVersion version, ISequenceProvider refProvider, string jsonKey, bool matchByAllele, bool isArray, int schemaVersion, bool isPositional, bool skipIncorrectRefEntries = true, bool throwErrorOnConflicts = false, int blockSize = SaCommon.DefaultBlockSize, GenomeAssembly assembly = GenomeAssembly.Unknown, bool leaveOpen = false)
{
_stream = nsaStream;
_indexStream = indexStream;
_writer = new ExtendedBinaryWriter(_stream, System.Text.Encoding.Default, leaveOpen);
_indexWriter = new ExtendedBinaryWriter(_indexStream, System.Text.Encoding.Default, leaveOpen);
_isPositional = isPositional;
_skipIncorrectRefEntries = skipIncorrectRefEntries;
_throwErrorOnConflicts = throwErrorOnConflicts;
_refProvider = refProvider;
_leaveOpen = leaveOpen;
assembly = _refProvider?.Assembly ?? assembly;
_block = new NsaBlock(new Zstandard(), blockSize);
_index = new NsaIndex(_indexWriter, assembly, version, jsonKey, matchByAllele, isArray, schemaVersion, isPositional);
_memBuffer = new byte[blockSize];
_memStream = new MemoryStream(_memBuffer);
_memWriter = new ExtendedBinaryWriter(_memStream);
}
