private CallabilityMetricsComputer(ILogger logger, CallabilityCalculator callability)
{
_logger = logger;
_callability = callability;
var metricsCollection = new StatCalculatorCollection <ReferenceInterval>
{
_callability,
};
_bedProcessor = new StatsProcessor <ReferenceInterval>(metricsCollection);
}
public static CallabilityMetricsComputer Create(ILogger logger, GenomeMetadata genomeMetadata, IFileLocation filterBed, bool isFemale)
{
var filterIntervals = LoadBedRegions(filterBed, genomeMetadata);
var nonFilterIntervals = GetIncludedIntervals(filterIntervals, genomeMetadata);
string chrY = genomeMetadata
.Contigs()
.Select(contig => contig.Name)
.SingleOrDefault(name => name == "chrY" || name == "Y");
if (isFemale && chrY != null)
{
nonFilterIntervals.Remove(chrY);
}
var callabilityCalculator = new CallabilityCalculator(nonFilterIntervals);
return(new CallabilityMetricsComputer(logger, callabilityCalculator));
}
