public PumiceValidator(string truthDirectory, string inputBamDirectory, bool makevcf, string outputDirectory, VariantCallMethod method, double minFreq = 0.0001, string program = null, string fixedArguments = null)
{
TruthBySample = new Dictionary <string, TruthItem>();
BamFiles = new List <string>();
_makevcf = makevcf;
_method = method;
_outputDirectory = outputDirectory;
_program = program;
_fixedArguments = fixedArguments;
_minFreq = minFreq;
var sampleTruthFiles = Directory.GetFiles(truthDirectory, "*_truth.txt");
foreach (var sampleTruthFile in sampleTruthFiles)
{
var tmpFileName = Path.GetFileNameWithoutExtension(sampleTruthFile);
var sampleId = tmpFileName.Split('_')[0];
//read truthFile
TruthItem t = new TruthItem(sampleTruthFile, sampleId);
TruthBySample.Add(sampleId, t);
var sampleBamFiles = Directory.GetFiles(inputBamDirectory, sampleId + "*.bam",
SearchOption.AllDirectories);
if (sampleBamFiles.Length <= 0)
{
continue;
}
BamFiles.AddRange(sampleBamFiles);
}
}
public VcfReader(string vcfPath, VariantCallMethod method)
{
var fileStream = new FileStream(vcfPath, FileMode.Open, FileAccess.Read, FileShare.Read);
_vcfStreamReader = new StreamReader(fileStream);
_method = method;
_isLofreq = _method == VariantCallMethod.Lofreq;
}
public Validator(List <string> bamFiles, Dictionary <string, TruthItem> truthBySample, VariantCallMethod method,
string outDir, double minFreq)
{
_bamFiles = bamFiles;
_truthBySample = truthBySample;
_method = method;
_minimumFreq = minFreq;
_outPutDir = outDir;
}
private void WriteToVariantLog(string rootFileName, VcfVariant variant, VariantCallMethod method, string type, StreamWriter writer)
{
writer.WriteLine($"{rootFileName}\t{variant.RefName}\t{variant.RefPosition}\t{variant.RefAllele}\t{variant.VariantAlleles[0]}\t" + method + $"\t{type}" + "\t" + variant.VariantFreq.ToString("0.####"));
}
