public override void MapReadToFeature(List <FeatureLocation> features, Dictionary <string, Dictionary <char, List <SAMAlignedLocation> > > chrStrandReadMap)
{
base.MapReadToFeature(features, chrStrandReadMap);
if (allowNTA)
{
//NTA has to be at the end of tRNA.
features.RemoveAll(m =>
{
m.SamLocations.RemoveAll(l =>
{
var loc = l.SamLocation;
if (!loc.Parent.Qname.Contains(SmallRNAConsts.NTA_TAG))
{
return(false);
}
var nta = loc.Parent.Qname.StringAfter(SmallRNAConsts.NTA_TAG);
if (nta.Length == 0)
{
return(false);
}
if (loc.End != l.FeatureLocation.End || !allowedNTAs.Contains(nta))
{
return(true);
}
if (nta.Equals("CC"))
{
return(!cca.Contains(loc.Parent.Qname.StringBefore(SmallRNAConsts.NTA_TAG)));
}
return(false);
});
return(m.SamLocations.Count == 0);
});
SmallRNAUtils.SelectBestMatchedNTA(features);
}
else
{
//all queries with NTA will be removed.
features.RemoveAll(m =>
{
m.SamLocations.RemoveAll(l =>
{
var loc = l.SamLocation;
if (!loc.Parent.Qname.Contains(SmallRNAConsts.NTA_TAG))
{
return(false);
}
var nta = loc.Parent.Qname.StringAfter(SmallRNAConsts.NTA_TAG);
return(nta.Length > 0);
});
return(m.SamLocations.Count == 0);
});
}
}
public override void MapReadToFeature(List <FeatureLocation> features, Dictionary <string, Dictionary <char, List <SAMAlignedLocation> > > chrStrandReadMap)
{
base.MapReadToFeature(features, chrStrandReadMap);
//For each query, keep the one with the best offset
var fsls = (from m in features
from l in m.SamLocations
select l).GroupBy(m => m.SamLocation.Parent).ToList().ConvertAll(m => m.ToArray());
//filter offset by priority
foreach (var fsl in fsls)
{
if (fsl.Count() == 1)
{
continue;
}
var bestOffset = fsl.Min(m => Options.Offsets.IndexOf(m.Offset));
foreach (var f in fsl)
{
if (Options.Offsets.IndexOf(f.Offset) != bestOffset)
{
f.FeatureLocation.SamLocations.Remove(f);
f.SamLocation.Features.Remove(f.FeatureLocation);
}
}
}
//filter NTA
if (hasNTA)
{
//remove all CCAA NTA which is designed for tRNA
features.RemoveAll(m =>
{
m.SamLocations.RemoveAll(s => s.SamLocation.Parent.Qname.StringAfter(SmallRNAConsts.NTA_TAG).Equals("CCAA"));
return(m.SamLocations.Count == 0);
});
SmallRNAUtils.SelectBestMatchedNTA(features);
}
}
