/// <summary>
/// Associates bam file with intervals to use. If no intervals applied, bam file will have no entry in the lookup.
/// </summary>
private void UpdateBamIntervals()
{
if (_options.IntervalPaths != null)
{
for (var i = 0; i < _options.BAMPaths.Length; i++)
{
var intervalFilePath = _options.IntervalPaths.Length == 1
? _options.IntervalPaths[0]
: _options.IntervalPaths[i];
try
{
var regionsByChr = new Dictionary <string, List <Region> >();
IntervalFileToRegion.ParseIntervalFile(intervalFilePath, regionsByChr);
// sort regions
/* now included in the parsing step
* foreach (var chrRegions in regionsByChr.Values)
* chrRegions.Sort((r1, r2) => r1.StartPosition.CompareTo(r2.StartPosition));
*/
_bamIntervalLookup[_options.BAMPaths[i]] = regionsByChr;
}
catch (Exception ex)
{
Logger.WriteToLog(
"Unable to load interval file '{0}'. No intervals will be applied to bam '{1}': {2}",
intervalFilePath, _options.BAMPaths[i], ex.Message);
}
}
}
}
public GeometricFilter(GeometricFilterParameters parameters)
{
IntervalFileToRegion.ParseIntervalFile(parameters.RegionOfInterestPath, _regionsByChr);
_mode = parameters.InclusionStrategy;
}
