public override IEnumerable <string> Process()
{
var result = new List <string>();
var builder = new ChromosomeCountSlimItemBuilder(options);
var chroms = builder.Build(options.InputFile);
Progress.SetMessage("Assigning query count ...");
var cm = options.GetCountMap();
var queries = chroms.GetQueries();
queries.ForEach(m =>
{
m.QueryCount = cm.GetCount(m.Qname);
});
Progress.SetMessage("Sorting items ...");
chroms.Sort((m1, m2) => m2.Queries.Count.CompareTo(m1.Queries.Count));
chroms.ForEach(m => m.Queries.Sort((m1, m2) => m1.Qname.CompareTo(m2.Qname)));
Progress.SetMessage("Saving xml file ...");
var mappedfile = options.OutputFile + ".mapped.xml";
new ChromosomeCountSlimItemXmlFormat().WriteToFile(mappedfile, chroms);
if (options.MergeChromosomesByReads)
{
chroms.MergeCalculateSortByEstimatedCount();
}
//new ChromosomeCountItemXmlFormat().WriteToFile(mappedfile + ".merged", chroms);
Progress.SetMessage("Saving count file ...");
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("Name\tUniqueQuery\tQueryCount");
foreach (var chr in chroms)
{
sw.WriteLine("{0}\t{1:0.##}\t{2}", (from m in chr.Names orderby m select m).Merge(";"),
chr.Queries.Count,
chr.GetQueryCount());
}
}
Progress.End();
return(result);
}
public override IEnumerable<string> Process()
{
var result = new List<string>();
var builder = new ChromosomeCountSlimItemBuilder(options);
var chroms = builder.Build(options.InputFile);
Progress.SetMessage("Assigning query count ...");
var cm = options.GetCountMap();
var queries = chroms.GetQueries();
queries.ForEach(m =>
{
m.QueryCount = cm.GetCount(m.Qname);
});
Progress.SetMessage("Sorting items ...");
chroms.Sort((m1, m2) => m2.Queries.Count.CompareTo(m1.Queries.Count));
chroms.ForEach(m => m.Queries.Sort((m1, m2) => m1.Qname.CompareTo(m2.Qname)));
Progress.SetMessage("Saving xml file ...");
var mappedfile = options.OutputFile + ".mapped.xml";
new ChromosomeCountSlimItemXmlFormat().WriteToFile(mappedfile, chroms);
if (options.MergeChromosomesByReads)
{
chroms.MergeCalculateSortByEstimatedCount();
}
//new ChromosomeCountItemXmlFormat().WriteToFile(mappedfile + ".merged", chroms);
Progress.SetMessage("Saving count file ...");
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("Name\tUniqueQuery\tQueryCount");
foreach (var chr in chroms)
{
sw.WriteLine("{0}\t{1:0.##}\t{2}", (from m in chr.Names orderby m select m).Merge(";"),
chr.Queries.Count,
chr.GetQueryCount());
}
}
Progress.End();
return result;
}
