public AmpliconBiasFileWriter CreateAmpliconBiasFileWriter(string outputVcfPath)
{
var writer = new AmpliconBiasFileWriter(outputVcfPath);
writer.WriteHeader();
return(writer);
}
public void Write()
{
var outFolder = Path.Combine(TestPaths.LocalScratchDirectory, "AmpliconBiasTestOutput");
var outputFile = Path.Combine(outFolder, "AmpliconBiasWriterTests.txt");
TestHelper.RecreateDirectory(outFolder);
//check writing
var chromosome = "chr1";
var reference = "A";
var alternate = "T";
var position = 123;
var BaseCalledAlleles = new List <CalledAllele>();
var variant = new CalledAllele(AlleleCategory.Snv)
{
Chromosome = chromosome,
ReferenceAllele = reference,
AlternateAllele = alternate,
ReferencePosition = position,
SupportByAmplicon = new Domain.Models.AmpliconCounts
{
AmpliconNames = new string[] { "Amplicon1", "Amplicon2", "Amplicon3" },
CountsForAmplicon = new int[] { 12, 4, 5 }
},
CoverageByAmplicon = new Domain.Models.AmpliconCounts
{
AmpliconNames = new string[] { "Amplicon1", "Amplicon2", "Amplicon3" },
CountsForAmplicon = new int[] { 120, 4000, 5000 }
}
};
AmpliconBiasCalculator.Compute(variant, 100, 0.01F);
BaseCalledAlleles.Add(variant);
var writer = new AmpliconBiasFileWriter(outputFile);
writer.WriteHeader();
writer.Write(BaseCalledAlleles);
writer.Dispose();
//check it reads in
//Chr,Position,Reference,Alternate,Name,freq,obs support, expected support, prob its real, confidence Qscore, bias detected ?, Filter Variant?
//chr1,123,A,T,Amplicon1,0.1,12,12,1,100,False,True,
//chr1,123,A,T,Amplicon2,0.001,4,400,2.06343002707725E-165,0,True,True,
//chr1,123,A,T,Amplicon3,0.001,5,500,1.87406134646469E-206,0,True,True,
var biasFileContents = File.ReadAllLines(outputFile);
Assert.True(biasFileContents.Length == 4);
var header = biasFileContents.First();
var expectedHeader = "Chr,Position,Reference,Alternate,Name,freq,obs support, expected support, prob its real, confidence Qscore, bias detected?, Filter Variant?";
var data = biasFileContents.Skip(1).First();
var expectedData = "chr1,123,A,T,Amplicon1,0.1,12,12,1,100,False,True,";
// Make sure well-formed and populated with the right data
Assert.Equal(expectedHeader, header);
Assert.Equal(expectedData, data);
//check IO
Assert.Throws <IOException>(() => writer.WriteHeader());
Assert.Throws <IOException>(() => writer.Write(BaseCalledAlleles));
writer.Dispose();
}
protected override void Initialize()
{
if (ShouldThrottle)
{
// one writer per bam
foreach (var workRequest in WorkRequests)
{
var vcfWriter = _factory.CreateVcfWriter(workRequest.OutputFilePath, new VcfWriterInputContext
{
ReferenceName = Genome.Directory,
QuotedCommandLineString = _factory.GetCommandLine(),
SampleName = Path.GetFileName(workRequest.BamFilePath),
ContigsByChr = Genome.ChromosomeLengths
});
if (_writeHeader)
{
vcfWriter.WriteHeader();
}
StrandBiasFileWriter sbBiasFileWriter = null;
AmpliconBiasFileWriter abBiasFileWriter = null;
if (_factory.Options.OutputBiasFiles)
{
sbBiasFileWriter = _factory.CreateStrandBiasFileWriter(workRequest.OutputFilePath);
abBiasFileWriter = _factory.CreateAmpliconBiasFileWriter(workRequest.OutputFilePath);
}
// use same writer across all chr. we will never be writing multiple chrs for a given bam at the same time
foreach (var chrName in Genome.ChromosomesToProcess)
{
var writerKey = GetChrOutputPath(workRequest, chrName);
_writerByChrLookup[writerKey] = vcfWriter;
_sbBiasWriterByChrLookup[writerKey] = sbBiasFileWriter;
_abBiasWriterByChrLookup[writerKey] = abBiasFileWriter;
}
_writers.Add(vcfWriter);
if (sbBiasFileWriter != null)
{
_sbBiasWriters.Add(sbBiasFileWriter);
}
if (abBiasFileWriter != null)
{
_abBiasWriters.Add(abBiasFileWriter);
}
}
}
else
{
// one writer per bam and per chr
// files will get stitched together later
foreach (var workRequest in WorkRequests)
{
foreach (var chrName in Genome.ChromosomesToProcess)
{
var outputPath = GetChrOutputPath(workRequest, chrName);
var vcfWriter = _factory.CreateVcfWriter(outputPath, new VcfWriterInputContext
{
ReferenceName = Genome.Directory,
QuotedCommandLineString = _factory.GetCommandLine(),
SampleName = Path.GetFileName(workRequest.BamFilePath),
ContigsByChr = Genome.ChromosomeLengths
});
StrandBiasFileWriter sbBiasFileWriter = null;
AmpliconBiasFileWriter abBiasFileWriter = null;
if (_factory.Options.OutputBiasFiles)
{
sbBiasFileWriter = _factory.CreateStrandBiasFileWriter(outputPath);
abBiasFileWriter = _factory.CreateAmpliconBiasFileWriter(outputPath);
}
var writerKey = outputPath;
_writerByChrLookup[writerKey] = vcfWriter;
_sbBiasWriterByChrLookup[writerKey] = sbBiasFileWriter;
_abBiasWriterByChrLookup[writerKey] = abBiasFileWriter;
_writers.Add(vcfWriter);
if (sbBiasFileWriter != null)
{
_sbBiasWriters.Add(sbBiasFileWriter);
}
if (abBiasFileWriter != null)
{
_abBiasWriters.Add(abBiasFileWriter);
}
}
}
}
}
