public ExitCodes Create()
{
var mimIdToEntry = new Dictionary <int, OmimImportEntry>();
AddOmimEntries(mimIdToEntry, _geneMap2Path);
AddOmimEntries(mimIdToEntry, _mim2GenePath);
UpdateGeneSymbols(mimIdToEntry);
var geneToOmimEntries = GetGeneToOmimEntries(mimIdToEntry);
var dataSourceVersion = DataSourceVersionReader.GetSourceVersion(_geneMap2Path + ".version");
using (var omimWriter = new GeneAnnotationTsvWriter(_outputDirectory, dataSourceVersion, null, 0, JsonKeyName, true))
{
foreach (var kvp in geneToOmimEntries.OrderBy(x => x.Key))
{
omimWriter.AddEntry(kvp.Key,
kvp.Value.OrderBy(x => x.MimNumber).Select(x => x.ToString()).ToList());
}
}
_geneSymbolUpdater.DisplayStatistics();
WriteUpdatedGeneSymbols();
return(ExitCodes.Success);
}
public GeneScoreTsvCreator(StreamReader reader, GeneAnnotationTsvWriter writer)
{
_reader = reader;
_writer = writer;
}
