public Genome SetGenome(ScyllaApplicationOptions options)
{
var bamChromosomes = new List <string>()
{
};
using (var reader = new BamReader(options.BamPath))
{
bamChromosomes = reader.GetReferenceNames();
}
return(new Genome(options.GenomePath, bamChromosomes));
}
public Factory(ScyllaApplicationOptions options)
{
_options = options;
if (options.GenomePath == null)
{
Logger.WriteWarningToLog("No reference genome was supplied by the user. All reference bases will be output as 'R'. ");
}
else
{
_genome = SetGenome(options);
}
}
public Factory(ScyllaApplicationOptions options)
{
_options = options;
}
