public IndexCreator(BlockGZipStream readStream, Stream writeStream)
{
_reader = new BgzipTextReader(readStream);
_writeStream = writeStream;
_chromBenchmark = new Benchmark();
_benchmark = new Benchmark();
}
public IndexCreator(BlockGZipStream readStream, Stream writeStream)
{
_reader = new BgzipTextReader(readStream);
_writeStream = writeStream;
_processedChromosome = new HashSet <string>();
_chromBenchmark = new Benchmark();
_benchmark = new Benchmark();
}
public void BgzipTextWriter_EndToEnd()
{
var asterisks = new string('*', BlockGZipStream.BlockGZipFormatCommon.BlockSize);
var observedLines = new List <string>();
var observedPositions = new List <long>();
using (var ms = new MemoryStream())
{
using (var stream = new BlockGZipStream(ms, CompressionMode.Compress, true))
using (var writer = new BgzipTextWriter(stream))
{
writer.Flush();
writer.WriteLine("BOB");
writer.WriteLine();
writer.Flush();
writer.Write("AB");
writer.Write("");
writer.Write("C");
writer.Write(" ");
writer.WriteLine("123");
writer.WriteLine(asterisks);
writer.WriteLine(asterisks);
writer.WriteLine(asterisks);
}
ms.Position = 0;
using (var reader = new BgzipTextReader(new BlockGZipStream(ms, CompressionMode.Decompress)))
{
while (true)
{
string line = reader.ReadLine();
observedPositions.Add(reader.Position);
if (line == null)
{
break;
}
observedLines.Add(line);
}
}
}
Assert.Equal(6, observedLines.Count);
Assert.Equal("BOB", observedLines[0]);
Assert.Equal(0, observedLines[1].Length);
Assert.Equal("ABC 123", observedLines[2]);
Assert.Equal(asterisks, observedLines[3]);
Assert.Equal(4, observedPositions[0]);
Assert.Equal(5, observedPositions[1]);
Assert.Equal(13, observedPositions[2]);
Assert.Equal(43843598, observedPositions[3]);
Assert.Equal(87097359, observedPositions[4]);
}
public void JasixStreamReader()
{
var stream = ResourceUtilities.GetReadStream(Resources.TopPath("TinyAnnotated.json"));
var lineCount = 0;
using (var jasixReader = new BgzipTextReader(stream))
{
while (jasixReader.ReadLine() != null)
{
lineCount++;
}
}
Assert.Equal(4, lineCount);
}
