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);
}
public IntervalTsvWriter(string outputPath, DataSourceVersion dataSourceVersion, string assembly, int dataVersion, string keyName,
ReportFor reportingFor)
{
var fileName = keyName + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".interval.tsv.gz";
_bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputPath, fileName));
_bgzipTextWriter.Write(GetHeader(dataSourceVersion, dataVersion, assembly, keyName, reportingFor));
_tsvIndex = new TsvIndex(Path.Combine(outputPath, fileName) + ".tvi");
}
public SaMiscTsvWriter(string outputPath, DataSourceVersion dataSourceVersion, string assembly, string keyName, ISequenceProvider sequenceProvider)
{
var fileName = keyName + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".misc.tsv.gz";
_bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputPath, fileName));
_bgzipTextWriter.Write(GetHeader(dataSourceVersion, assembly));
_tsvIndex = new TsvIndex(Path.Combine(outputPath, fileName + ".tvi"));
_sequenceProvider = sequenceProvider;
}
private SaTsvWriter(string outputDir, DataSourceVersion dataSourceVersion, string assembly, int schemaVersion,
string jsonKey, string vcfKeys,
bool isAlleleSpecific, bool isArray = false)
{
var fileName = jsonKey + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".tsv.gz";
_bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputDir, fileName));
_bgzipTextWriter.Write(GetHeader(dataSourceVersion, schemaVersion, assembly, jsonKey, vcfKeys, isAlleleSpecific, isArray));
_tsvIndex = new TsvIndex(Path.Combine(outputDir, fileName + ".tvi"));
}
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 JsonWriter(StreamWriter writer, Stream indexStream, string annotator, string creationTime, string vepDataVersion,
List <IDataSourceVersion> dataSourceVersions, string genomeAssembly, string[] sampleNames, bool leaveOpen)
{
_writer = writer;
_writer.NewLine = "\n";
_firstEntry = true;
_positionFieldClosed = false;
_leaveOpen = leaveOpen;
_bgzipTextWriter = writer as BgzipTextWriter;
_jasixIndexCreator = _bgzipTextWriter != null
? new OnTheFlyIndexCreator(indexStream)
: null;
WriteHeader(annotator, creationTime, genomeAssembly, JsonCommon.SchemaVersion, vepDataVersion,
dataSourceVersions, sampleNames);
}
