static void Main(string[] args)
{
/*
* ExACAnnotator.GetVarAnnotation("1", 931393, "G", "T");
* ExACAnnotator.GetVarAnnotation("1-935222-C-A");
* ExACAnnotator.GetVarAnnotation("14-21853913-T-C");
* ExACAnnotator.GetVarAnnotation("22-46615746-A-G");
* ExACAnnotator.GetVarAnnotation("1-6475586-TC-GA");
* List<string> list = new List<string>();
* list.Add("1-931393-G-T");
* list.Add("14-21853913-T-C");
* list.Add("22-46615746-A-G");
* list.Add("1-6475586-TC-GA");
* ExACAnnotator.GetBulkVarAnnotations(list);*/
if (args.Length != 2)
{
Console.WriteLine("Please use:\ndotnet run yourfile.vcf output.txt");
return;
}
string vcfFile = args[0];
if (!File.Exists(vcfFile))
{
Console.WriteLine("Error! Can not find vcf file to annotate: " + vcfFile);
return;
}
string outputFile = args[1];
IVcfAnnotator annot = new ExACAnnotator();
VCFFile vf = new VCFFile(vcfFile);
annot.AnnotateVcfFile(vf, outputFile);
vf.Close();
}
public Dictionary <string, IVarAnnotation> BulkAnnotateVars(string[] queries)
{
Dictionary <string, ExACVariantAnnotation> dict = ExACAnnotator.GetBulkVarAnnotations(queries);
Dictionary <string, IVarAnnotation> outputs = new Dictionary <string, IVarAnnotation>();
foreach (KeyValuePair <string, ExACVariantAnnotation> pair in dict)
{
outputs[pair.Key] = pair.Value;
}
return(outputs);
}
public IVarAnnotation AnnotateVar(string query)
{
return(ExACAnnotator.GetVarAnnotation(query));
}
