public override IEnumerable<string> Process()
{
var data = new CnMOPsItemReader().ReadFromFile(options.InputFile);
Dictionary<string, List<ItemRange>> result = MergeRange(data);
var seqnames = result.Keys.OrderBy(m => m).ToList();
GenomeUtils.SortChromosome(seqnames, l => l, l => 1);
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("seqname\tstart\tend\tlocus\tsample\tsample_start\tsample_end\tsample_type");
foreach (var seqname in seqnames)
{
var ranges = result[seqname];
foreach (var range in ranges)
{
foreach (var cn in range.Items)
{
if (options.IgnoreCN1CN3 && (cn.CN.Equals("CN1") || cn.CN.Equals("CN3")))
{
continue;
}
sw.WriteLine("{0}\t{1}\t{2}\t{0}:{1}-{2}\t{3}\t{4}\t{5}\t{6}",
seqname, range.Start, range.End, cn.FileName, cn.Start, cn.End, cn.CN);
}
}
}
}
var filenames = (from d in data select d.FileName).Distinct().OrderBy(l => l).ToArray();
using (var sw = new StreamWriter(options.OutputFile + ".cnvr"))
{
sw.WriteLine("seqname\tstart\tend\tfile\t{0}", filenames.Merge("\t"));
foreach (var seqname in seqnames)
{
var ranges = result[seqname];
foreach (var range in ranges)
{
var cns = (from filename in filenames
let cn = range.Items.Where(l => l.FileName.Equals(filename)).FirstOrDefault()
select cn == null ? "CN2" : cn.CN).ToArray();
if (options.IgnoreCN1CN3 && cns.All(l => l.Equals("CN1") || l.Equals("CN2") || l.Equals("CN3")))
{
continue;
}
sw.WriteLine("{0}\t{1}\t{2}\t{0}_{1}_{2}\t{3}",
seqname, range.Start, range.End, cns.Merge("\t"));
}
}
}
return new[] { options.OutputFile, options.OutputFile + ".cnvr" };
}
public void Test()
{
var data = new CnMOPsItemReader().ReadFromFile("../../../data/cnmops.txt");
var focus_before = data.Where(l => l.Start > 3000000 && l.End < 9000000).ToList();
var ranges = CnMOPSCallProcessor.MergeRange(focus_before);
var focus = ranges["5"];
Assert.AreEqual(1, focus.Count);
Assert.AreEqual(3000100, focus[0].Start);
Assert.AreEqual(8494963, focus[0].End);
//focus.ForEach(l =>
//{
// Console.WriteLine("{0}-{1}", l.Start, l.End);
// l.Items.ForEach(m =>
// {
// Console.WriteLine("\t{0}-{1}\t{2}\t{3}", m.Start, m.End, m.FileName, m.CN);
// });
//});
}
