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)); }