public void Begin_end_section_and_readback()
{
var index = new JasixIndex();
const string section = "section1";
index.BeginSection(section, 0);
Assert.Throws <UserErrorException>(() => index.BeginSection(section, 1));
index.EndSection(section, 100);
Assert.Throws <UserErrorException>(() => index.EndSection(section, 101));
Assert.Equal(0, index.GetSectionBegin(section));
Assert.Equal(100, index.GetSectionEnd(section));
}
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);
}
private string IndexPositions(JasixIndex index)
{
// we need the location before accessing the line
long linePosition = _reader.Position;
index.BeginSection(JasixCommons.PositionsSectionTag, linePosition);
Console.WriteLine($"section:{JasixCommons.PositionsSectionTag} starts at {linePosition}");
var previousChr = "";
var previousPos = 0;
string line;
while ((line = _reader.ReadLine()) != null)
{
if (line.OptimizedStartsWith(']'))
{
index.EndSection(JasixCommons.PositionsSectionTag, linePosition);
Console.WriteLine($"section:{JasixCommons.PositionsSectionTag} ends at {linePosition}");
break;
}
line = line.TrimEnd(',');
(string chr, int position, int end) = GetChromPosition(line);
CheckSorting(chr, position, previousChr, previousPos);
index.Add(chr, position, end, linePosition);
linePosition = _reader.Position;
previousChr = chr;
previousPos = position;
}
return(line);
}
private void IndexHeader(JasixIndex index)
{
string searchTag = $"\"{JasixCommons.PositionsSectionTag}\":[";
string headerTag = $"{{\"{JasixCommons.HeaderSectionTag}\":";
string line;
long previousPosition = _reader.Position;
while ((line = _reader.ReadLine()) != null)
{
if (line.StartsWith(headerTag))
{
index.BeginSection(JasixCommons.HeaderSectionTag, previousPosition);
Console.WriteLine($"section:{JasixCommons.HeaderSectionTag} starts at {previousPosition}");
}
if (line.EndsWith(searchTag))
{
{
index.EndSection(JasixCommons.HeaderSectionTag, previousPosition);
Console.WriteLine($"section:{JasixCommons.HeaderSectionTag} ends at {previousPosition}");
}
break;
}
previousPosition = _reader.Position;
}
}
private void IndexGenes(string lastLine, JasixIndex index)
{
if (lastLine == null)
{
return;
}
do
{
long linePosition = _reader.Position;
if (lastLine.EndsWith($",\"{JasixCommons.GenesSectionTag}\":["))
{
index.BeginSection(JasixCommons.GenesSectionTag, _reader.Position);
Console.WriteLine($"section:{JasixCommons.GenesSectionTag} starts at {_reader.Position}");
}
if (lastLine.EndsWith("]}"))
{
index.EndSection(JasixCommons.GenesSectionTag, linePosition);
Console.WriteLine($"section:{JasixCommons.GenesSectionTag} ends at {linePosition}");
break;
}
} while ((lastLine = _reader.ReadLine()) != null);
}
public void BeginSection(string sectionName, long fileLocation)
{
_jasixIndex.BeginSection(sectionName, fileLocation);
}