public override IEnumerable<string> Process()
{
var reader = new SamToolsStatItemReader();
var items = (from file in options.GetStatisticFiles()
let filename = Path.GetFileNameWithoutExtension(file)
let shortname = filename.ToLower().EndsWith(".bam") ? Path.GetFileNameWithoutExtension(filename) : filename
select new
{
FileName = shortname,
Data = reader.ReadFromFile(file)
}).ToList();
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("Sample\tTotalReads\tMappedReads\tMappedReadPercentage\tMappedPairs");
foreach (var item in items)
{
sw.WriteLine("{0}\t{1}\t{2}\t{3:0.00}%\t{4}",
item.FileName,
item.Data.Total,
item.Data.Mapped,
item.Data.Mapped * 100.0 / item.Data.Total,
item.Data.WithItselfAndMateMapped);
}
}
return new string[] { options.OutputFile };
}
public void TestMethod()
{
var item = new SamToolsStatItemReader().ReadFromFile(@"../../../data/2476-JP-01.bam.stat");
Assert.AreEqual(122383979, item.Total);
Assert.AreEqual(0, item.Duplicates);
Assert.AreEqual(122092264, item.Mapped);
Assert.AreEqual(122383979, item.PairedInSequencing);
Assert.AreEqual(61183108, item.Read1);
Assert.AreEqual(61200871, item.Read2);
Assert.AreEqual(121137215, item.ProperlyPaired);
Assert.AreEqual(121839842, item.WithItselfAndMateMapped);
Assert.AreEqual(252422, item.Singletons);
Assert.AreEqual(482135, item.WithMateMappedToADifferentChr);
Assert.AreEqual(375411, item.WithMateMappedToADifferentChrMapQ);
}
