public static Dictionary <string, OptionSet> GetParsingMethods(GeometricFilterParameters options)
{
var requiredOps = new OptionSet
{
{
"ROI=",
OptionTypes.STRING + " Full path for region of interest file.",
value => options.RegionOfInterestPath = value
},
};
var commonOps = new OptionSet
{
{
"InclusionModel=",
OptionTypes.STRING + " How to determine if variants are in the region of interest. Use 'start' for by variant start position, and 'expand' to automatically expand the reporting region to include any variants which overlap the input ROI.",
value => options.InclusionStrategy = ConvertToInclusionModel(value)
},
};
var optionDict = new Dictionary <string, OptionSet>
{
{ "REQUIRED", requiredOps },
{ "COMMON", commonOps },
};
return(optionDict);
}
public GeometricFilter(GeometricFilterParameters parameters)
{
IntervalFileToRegion.ParseIntervalFile(parameters.RegionOfInterestPath, _regionsByChr);
_mode = parameters.InclusionStrategy;
}