public void AddEntry(string chromosome, int position, string refAllele, string altAllele, string vcfString, List <string> jsonStrings)
{
if ((jsonStrings == null || jsonStrings.Count == 0) && string.IsNullOrEmpty(vcfString))
{
return;
}
//validate the vcf reference
if (!ValidateReference(chromosome, position, refAllele))
{
return;
}
if (!chromosome.Equals(_currentChromosome))
{
_tsvIndex.AddTagPosition(chromosome, _bgzipTextWriter.Position);
// Console.WriteLine($"chr {chromosome}, filePos: {_bgzipTextWriter.Position}");
_currentChromosome = chromosome;
}
refAllele = string.IsNullOrEmpty(refAllele) ? "-" : refAllele;
altAllele = string.IsNullOrEmpty(altAllele) ? "-" : altAllele;
_bgzipTextWriter.Write($"{chromosome}\t{position}\t{refAllele}\t{altAllele}\t{vcfString}");
if (jsonStrings != null)
{
foreach (var jsonString in jsonStrings)
{
_bgzipTextWriter.Write($"\t{jsonString}");
}
}
_bgzipTextWriter.Write("\n");
}
public void AddEntry(string chromosome, int start, int end, string jsonString)
{
if (string.IsNullOrEmpty(jsonString))
{
return;
}
if (chromosome != _currentChromosome)
{
_tsvIndex.AddTagPosition(chromosome, _bgzipTextWriter.Position);
_currentChromosome = chromosome;
}
_bgzipTextWriter.Write($"{chromosome}\t{start}\t{end}\t{jsonString}\n");
}
public void AddEntry(string chromosome, int position, string globalMajorAllele, string refAllele)
{
if (globalMajorAllele == null)
{
throw new Exception($"no global major allele for {chromosome}:{position}");
}
//validate the vcf reference
if (!ValidateReference(chromosome, position, refAllele))
{
return;
}
if (!chromosome.Equals(_currentChromosome))
{
_tsvIndex.AddTagPosition(chromosome, _bgzipTextWriter.Position);
//Console.WriteLine($"chr {chromosome}, filePos: {_bgzipTextWriter.Position}");
_currentChromosome = chromosome;
}
_bgzipTextWriter.Write($"{chromosome}\t{position}\t{globalMajorAllele}\n");
}