コード例 #1
0
        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);
        }
コード例 #2
0
ファイル: NsaWriter.cs プロジェクト: wangdi2014/Nirvana
        //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);
        }