public void Open(string normalFile, string tumorFile)
{
GetChromosomes(normalFile);
normal = new AlignedPositionMapBuilder(options, normalFile);
tumor = new AlignedPositionMapBuilder(options, tumorFile);
}
public void Open(string normalFile, string tumorFile)
{
GetChromosomes(normalFile);
normal = new AlignedPositionMapBuilder(options, normalFile);
tumor = new AlignedPositionMapBuilder(options, tumorFile);
}
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);
// }
//}
}
}