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));
}
private void WriteOutput(IAnnotatedPosition annotatedPosition, long textWriterPosition,
OnTheFlyIndexCreator jasixIndexCreator, IJsonWriter jsonWriter, LiteVcfWriter vcfWriter,
LiteVcfWriter gvcfWriter, string jsonOutput)
{
jasixIndexCreator.Add(annotatedPosition.Position, textWriterPosition);
jsonWriter.WriteJsonEntry(jsonOutput);
if (vcfWriter == null && gvcfWriter == null || annotatedPosition.Position.IsRecomposed)
{
return;
}
string vcfLine = _conversion.Convert(annotatedPosition);
vcfWriter?.Write(vcfLine);
gvcfWriter?.Write(vcfLine);
}
public void WriteJsonEntry(IPosition position, string entry)
{
if (string.IsNullOrEmpty(entry))
{
return;
}
_jasixIndexCreator?.Add(position, _bgzipTextWriter.Position);
if (!_firstEntry)
{
_writer.WriteLine(",");
}
else
{
_jasixIndexCreator?.BeginSection(JasixCommons.PositionsSectionTag, _bgzipTextWriter.Position);
}
_firstEntry = false;
_writer.Write(entry);
}