//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);
}
//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);
}