public AlignedPositionMapBuilder(AlignedPositionMapBuilderOptions options, string fileName) { this._options = options; _format = options.GetSAMFormat(); _file = SAMFactory.GetReader(fileName, true); _list = new AlignedPositionMapList(); _done = new List<AlignedPositionMap>(); }
public AlignedPositionMapBuilder(AlignedPositionMapBuilderOptions options, string fileName) { this._options = options; _format = options.GetSAMFormat(); _file = SAMFactory.GetReader(fileName, true); _list = new AlignedPositionMapList(); _done = new List <AlignedPositionMap>(); }
public static ISAMFile GetReader(string filename, bool skipHeaders = false, string rangeInBedFile = null) { ISAMFile result = null; if (SAMUtils.IsBAMFile(filename) && !SystemUtils.IsLinux) { result = new BAMWindowReader(filename); } else { result = new SAMLinuxReader("samtools", filename, rangeInBedFile); } if (skipHeaders) { result.ReadHeaders(); } return(result); }