private static (Stream jsonStream, Stream jasixStream) GetNirvanaJsonStreamWithoutGenes(int chromNumber)
{
var jsonStream = new MemoryStream();
var jasixStream = new MemoryStream();
using (var bgZipStream = new BlockGZipStream(jsonStream, CompressionMode.Compress, true))
using (var writer = new BgzipTextWriter(bgZipStream))
using (var jasixIndex = new JasixIndex())
{
writer.Write(NirvanaHeader);
writer.Flush();
jasixIndex.BeginSection(JasixCommons.PositionsSectionTag, writer.Position);
for (int i = 100 * chromNumber; i < 123 * chromNumber; i++)
{
writer.WriteLine($"{{\"chromosome\":\"chr{chromNumber}\",\"position\":{i}}},");
if (i % 50 == 0)
{
writer.Flush(); //creating another block
}
}
writer.WriteLine($"{{\"chromosome\":\"chr{chromNumber}\",\"position\":{100 *chromNumber +25}}}");
writer.Flush();
jasixIndex.EndSection(JasixCommons.PositionsSectionTag, writer.Position);
writer.Write(NirvanaFooter);
jasixIndex.Write(jasixStream);
}
jsonStream.Position = 0;
jasixStream.Position = 0;
return(jsonStream, jasixStream);
}
// due to the flush, the end of a section will point to the next to last block for a section.
// e.g. if positions start at block 2 and end at block 10, blocks 2..9 contains positions.
private void BeginSection(string section)
{
if (_bgzipTextWriter == null)
{
return;
}
_bgzipTextWriter.Flush();
_jasixIndexCreator.BeginSection(section, _bgzipTextWriter.Position);
}
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]);
}
