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 void TestMappingQuality() { var options = new AlignedPositionMapBuilderOptions(); options.MinimumReadQuality = 255; var builder = new AlignedPositionMapBuilder(options, "../../../data/small_2.sam"); var item = builder.Next(); //the maximum MapQ is 50, so no reads passed the criteria Assert.IsNull(item); options.MinimumReadQuality = 5; builder = new AlignedPositionMapBuilder(options, "../../../data/small_2.sam"); item = builder.Next(); Assert.IsNotNull(item); }
public void TestPileup() { var options = new AlignedPositionMapBuilderOptions(); options.MinimumReadQuality = 5; var builder = new AlignedPositionMapBuilder(options, "../../../data/small_2.sam"); AlignedPositionMap item; while ((item = builder.Next()) != null) { if (3589590 == item.Position) { Assert.IsTrue(item.ContainsKey("T")); Assert.AreEqual(2, item["T"].Count); Assert.AreEqual(40, (int)item["T"][0].Score - 33); Assert.AreEqual(39, item["T"][0].Distance); Assert.AreEqual(41, (int)item["T"][1].Score - 33); Assert.AreEqual(22, item["T"][1].Distance); Assert.IsTrue(item.ContainsKey("INSERTION_T")); Assert.AreEqual(1, item["INSERTION_T"].Count); Assert.AreEqual(41, (int)item["INSERTION_T"][0].Score - 33); Assert.AreEqual(21, item["INSERTION_T"][0].Distance); } if (3589733 == item.Position) { Assert.IsTrue(item.ContainsKey("A")); Assert.AreEqual(2, item["A"].Count); Assert.AreEqual(41, (int)item["A"][0].Score - 33); Assert.AreEqual(71, item["A"][0].Distance); Assert.AreEqual(36, (int)item["A"][1].Score - 33); Assert.AreEqual(12, item["A"][1].Distance); Assert.IsTrue(item.ContainsKey("C")); Assert.AreEqual(1, item["C"].Count); Assert.AreEqual(9, (int)item["C"][0].Score - 33); Assert.AreEqual(48, item["C"][0].Distance); } //Console.WriteLine(item.Position); //foreach (var eve in item) //{ // foreach (var p in eve.Value) // { // Console.WriteLine("\t{0}\t{1}\t{2}\t{3}", eve.Key, (int)p.Score - 33, p.Distance, p.EventLength); // } //} } }