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 void SortByNameAndScore <T>(this List <T> list, ISAMFormat format) where T : ISAMItem { list.Sort((m1, m2) => { var result = m1.Qname.CompareTo(m2.Qname); if (result == 0) { result = format.CompareScore(m1.AlignmentScore, m2.AlignmentScore); } return(result); }); }
/// <summary> /// The default constructor which chooses the default encoding based on the alphabet. /// </summary> public SAMAlignedItemBAMParser(ISAMFormat samformat, string bamFileName, string refSeqName) : base(bamFileName, refSeqName) { Format = samformat; }