private void WriteJson(IAnnotatedVariant annotatedVariant, IAnnotatedAlternateAllele firstAllele,
UnifiedJsonWriter writer)
{
if (firstAllele.IsReference && !firstAllele.IsReferenceMinor && !firstAllele.IsReferenceNoCall)
{
return;
}
writer.Write(annotatedVariant.ToString());
}
private static void WriteOmim(IAnnotationSource annotator, UnifiedJsonWriter unifiedJsonWriter)
{
var omimAnnotations = new List <string>();
annotator.AddGeneLevelAnnotation(omimAnnotations);
var annotionOutput = UnifiedJson.GetGeneAnnotation(omimAnnotations, "omim");
unifiedJsonWriter.Write(annotionOutput);
}
public void UnifiedJsonWriterTest()
{
var randomPath = GetRandomPath();
using (var streamWriter = new StreamWriter(FileUtilities.GetCreateStream(randomPath)))
using (var writer = new UnifiedJsonWriter(streamWriter, DateTime.Now.ToString(CultureInfo.InvariantCulture), "testing", null, null, null))
{
writer.Write("test json string");
}
File.Delete(randomPath);
}
private void WriteOutput(string vcfOutput, IAnnotatedVariant annotatedVariant, LiteVcfWriter vcfWriter,
LiteVcfWriter gvcfWriter, UnifiedJsonWriter jsonWriter)
{
if (ConfigurationSettings.Gvcf)
{
WriteGvcf(vcfOutput, gvcfWriter);
}
if (annotatedVariant?.AnnotatedAlternateAlleles == null ||
annotatedVariant.AnnotatedAlternateAlleles.Count == 0)
{
return;
}
var firstAllele = annotatedVariant.AnnotatedAlternateAlleles[0];
WriteJson(annotatedVariant, firstAllele, jsonWriter);
if (ConfigurationSettings.Vcf)
{
WriteVcf(vcfOutput, firstAllele, vcfWriter);
}
}
