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);
}
public void CreateIndex()
{
var searchTag = $"\"{SectionToIndex}\":[";
const string headerTag = "{\"header\":";
var index = new JasixIndex();
string line;
//skipping lines before the sectionToIndex arrives
while ((line = _reader.ReadLine()) != null)
{
if (line.StartsWith(headerTag))
{
index.HeaderLine = ExtractHeader(line);
}
if (line.EndsWith(searchTag))
{
break;
}
}
// we need the location before accessing the line
var fileLoc = _reader.Position;
string previousChr = "";
int previousPos = 0;
while ((line = _reader.ReadLine()) != null)
{
if (line.StartsWith("]"))
{
break;
}
line = line.TrimEnd(',');
var chrPos = GetChromPosition(line);
CheckFileSorted(chrPos.chr, chrPos.position, previousChr, previousPos);
index.Add(chrPos.chr, chrPos.position, chrPos.end, fileLoc);
fileLoc = _reader.Position;
previousChr = chrPos.chr;
previousPos = chrPos.position;
}
index.Write(_writeStream);
Console.WriteLine();
var peakMemoryUsageBytes = MemoryUtilities.GetPeakMemoryUsage();
var wallTimeSpan = _benchmark.GetElapsedTime();
Console.WriteLine();
if (peakMemoryUsageBytes > 0)
{
Console.WriteLine("Peak memory usage: {0}", MemoryUtilities.ToHumanReadable(peakMemoryUsageBytes));
}
Console.WriteLine("Time: {0}", Benchmark.ToHumanReadable(wallTimeSpan));
}
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 void JasixStreamReader()
{
var stream = ResourceUtilities.GetReadStream(Resources.TopPath("TinyAnnotated.json"));
var lineCount = 0;
using (var jasixReader = new BgzipTextReader(stream))
{
while (jasixReader.ReadLine() != null)
{
lineCount++;
}
}
Assert.Equal(4, lineCount);
}
