public override IEnumerable <string> Process()
{
var result = new List <string>();
var samformat = _options.GetEngineFormat();
var format = new MappedItemGroupXmlFileFormat();
Progress.SetMessage("reading mapped reads from " + _options.InputFile1 + " ...");
var items1 = format.ReadFromFile(_options.InputFile1);
Progress.SetMessage("reading mapped reads from " + _options.InputFile2 + " ...");
var items2 = format.ReadFromFile(_options.InputFile2);
var reads1 = items1.GetQueries().ToDictionary(m => m.Qname);
var reads2 = items2.GetQueries().ToDictionary(m => m.Qname);
var qnames = reads1.Keys.Union(reads2.Keys).Distinct().ToList();
foreach (var qname in qnames)
{
if (!reads1.ContainsKey(qname) || !reads2.ContainsKey(qname))
{
continue;
}
var r1 = reads1[qname];
var r2 = reads2[qname];
var res = samformat.CompareScore(r1.AlignmentScore, r2.AlignmentScore);
if (res == 0)
{
items1.RemoveRead(qname);
items2.RemoveRead(qname);
}
else if (res < 0)
{
items2.RemoveRead(qname);
}
else
{
items1.RemoveRead(qname);
}
}
var writer = new MappedItemGroupSequenceWriter();
SaveItems(items1, _options.OutputFile1, writer, format, result);
SaveItems(items2, _options.OutputFile2, writer, format, result);
return(result);
}
private static void SaveItems(List <MappedItemGroup> items1, string outputFile, MappedItemGroupSequenceWriter writer,
MappedItemGroupXmlFileFormat format, List <string> result)
{
items1.RemoveAll(m => m.QueryCount == 0);
var xml1 = outputFile + ".xml";
if (items1.Any(m => m.Name.Contains(".tRNA")))
{
items1.SortTRna();
}
writer.WriteToFile(outputFile, items1);
format.WriteToFile(xml1, items1);
result.Add(outputFile);
result.Add(xml1);
}