public AlignmentSource(IAlignmentExtractor alignmentExtractor,
IAlignmentMateFinder mateFinder,
AlignmentSourceConfig config) // add intervals
{
_alignmentExtractor = alignmentExtractor;
_mateFinder = mateFinder;
_config = config;
}
public BamFileAlignmentExtractor(string bamFilePath, string chromosomeFilter = null,
Dictionary <string, List <Region> > bamIntervals = null,
IAlignmentMateFinder mateFinder = null)
{
if (!File.Exists(bamFilePath))
{
throw new ArgumentException(string.Format("Bam file '{0}' does not exist.", bamFilePath));
}
if (!File.Exists(bamFilePath + ".bai"))
{
throw new ArgumentException(string.Format("Bai file '{0}.bai' does not exist.", bamFilePath));
}
_bamFilePath = bamFilePath;
_remainingIntervals = bamIntervals == null ? null : Copy(bamIntervals);
_mateFinder = mateFinder;
InitializeReader(chromosomeFilter);
}