public void TestRead()
{
var filename = @"../../../data/01-018-Post_CTTGTA_slim.sam";
var builder = new SAMAlignedItemCandidateBuilder(1);
HashSet<string> totalQueryNames;
var items = builder.Build<TrimedSAMAlignedItem>(filename, out totalQueryNames);
Assert.AreEqual(3, items.Count);
Assert.AreEqual("HWI-ST508:279:D2BAFACXX:5:1101:12662:2102", items[0].Qname);
Assert.AreEqual("HWI-ST508:279:D2BAFACXX:5:1101:16014:2180", items[1].Qname);
Assert.AreEqual("HWI-ST508:279:D2BAFACXX:5:1101:20077:2189", items[2].Qname);
Assert.AreEqual(7, items[0].Locations.Count);
Assert.AreEqual(6, items[1].Locations.Count);
Assert.AreEqual(1, items[2].Locations.Count);
}
public void TestFill()
{
var samfile = @"../../../data/01-018-Post_CTTGTA_slim.sam";
var fastqfile = @"../../../data/01-018-Post_CTTGTA_slim.fastq";
var builder = new SAMAlignedItemCandidateBuilder(1);
HashSet<string> totalQueryNames;
var items = builder.Build<TrimedSAMAlignedItem>(samfile, out totalQueryNames);
items.FillOriginalSequence(fastqfile);
Assert.AreEqual("GAGGACCGGGATGGACATAC", items[0].OriginalSequence, items[0].Qname);
Assert.AreEqual("ATACCGTCGTAGTCTTAACC", items[1].OriginalSequence, items[1].Qname);
Assert.AreEqual("AAGGATTGACAGATTGAGAGC", items[2].OriginalSequence, items[2].Qname);
Assert.AreEqual(items[0].OriginalSequence.Substring(2).Substring(0, items[0].OriginalSequence.Length - 5), items[0].Sequence, items[0].Qname);
Assert.AreEqual(items[1].OriginalSequence.Substring(2).Substring(0, items[1].OriginalSequence.Length - 5), items[1].Sequence, items[1].Qname);
Assert.AreEqual(items[2].OriginalSequence.Substring(2).Substring(0, items[2].OriginalSequence.Length - 5), items[2].Sequence, items[2].Qname);
}