private void WriteHeader(string annotator, string creationTime, string genomeAssembly, int schemaVersion,
string vepDataVersion, IEnumerable <IDataSourceVersion> dataSourceVersions, string[] sampleNames)
{
_jasixIndexCreator?.BeginSection(JasixCommons.HeaderSectionTag, _bgzipTextWriter.Position);
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
sb.Append($"{{\"{JasixCommons.HeaderSectionTag}\":{{");
jsonObject.AddStringValue("annotator", annotator);
jsonObject.AddStringValue("creationTime", creationTime);
jsonObject.AddStringValue("genomeAssembly", genomeAssembly);
jsonObject.AddIntValue("schemaVersion", schemaVersion);
jsonObject.AddStringValue("dataVersion", vepDataVersion);
jsonObject.AddObjectValues("dataSources", dataSourceVersions);
if (sampleNames != null)
{
jsonObject.AddStringValues("samples", sampleNames);
}
sb.Append($"}},\"{JasixCommons.PositionsSectionTag}\":[\n");
_writer.Write(StringBuilderCache.GetStringAndRelease(sb));
_writer.Flush();
_jasixIndexCreator?.EndSection(JasixCommons.HeaderSectionTag, _bgzipTextWriter.Position - 1);
}
public void Add_one_chrom()
{
var position1 = new Mock <IPosition>();
position1.SetupGet(x => x.Chromosome).Returns(ChromosomeUtilities.Chr1);
position1.SetupGet(x => x.Start).Returns(100);
position1.SetupGet(x => x.RefAllele).Returns("A");
position1.SetupGet(x => x.AltAlleles).Returns(new [] { "C" });
var memStream = new MemoryStream();
using (var indexCreator = new OnTheFlyIndexCreator(memStream))
{
indexCreator.BeginSection("positions", 100);
indexCreator.Add(position1.Object, 2588);
indexCreator.EndSection("positions", 2699);
}
var readStream = new MemoryStream(memStream.ToArray());
readStream.Seek(0, SeekOrigin.Begin);
var index = new JasixIndex(readStream);
Assert.Equal(100, index.GetSectionBegin("positions"));
Assert.Equal(2588, index.GetFirstVariantPosition("chr1", 100, 102));
}
// 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);
}