public virtual void MapReadToFeature(List <FeatureLocation> features, Dictionary <string, Dictionary <char, List <SAMAlignedLocation> > > chrStrandReadMap)
{
if (chrStrandReadMap.Count == 0 || features.Count == 0)
{
return;
}
//mapping to genome, considering offset limitation
//Progress.SetRange(0, smallRNAs.Count);
foreach (var smallRNA in features)
{
//Progress.Increment(1);
Dictionary <char, List <SAMAlignedLocation> > curMatchedMap;
if (!chrStrandReadMap.TryGetValue(smallRNA.Seqname, out curMatchedMap))
{
continue;
}
//mapped query must have same oritation with miRNA defined at gff or bed file.
var matches = curMatchedMap[smallRNA.Strand];
foreach (var m in matches)
{
var r = AcceptLocationPair(smallRNA, m);
if (r.Accepted)
{
var fsl = new FeatureSamLocation(smallRNA);
fsl.SamLocation = m;
fsl.NumberOfMismatch = r.NumberOfMismatch;
fsl.NumberOfNoPenaltyMutation = r.NumberOfNoPenaltyMutation;
fsl.OverlapPercentage = r.OverlapPercentage;
}
}
}
}
private void DoMapReadToSequenceRegionWithOrientation(List <FeatureLocation> mapped, List <SAMAlignedItem> reads)
{
//build chr/strand/samlist map
Progress.SetMessage("building chr/strand/samlist map ...");
var chrStrandMatchedMap = new Dictionary <string, Dictionary <char, List <SAMAlignedLocation> > >();
foreach (var read in reads)
{
foreach (var loc in read.Locations)
{
Dictionary <char, List <SAMAlignedLocation> > map;
if (!chrStrandMatchedMap.TryGetValue(loc.Seqname, out map))
{
map = new Dictionary <char, List <SAMAlignedLocation> >();
map['+'] = new List <SAMAlignedLocation>();
map['-'] = new List <SAMAlignedLocation>();
chrStrandMatchedMap[loc.Seqname] = map;
}
map[loc.Strand].Add(loc);
}
}
Progress.SetRange(0, mapped.Count);
var gmapped = new Dictionary <string, SAMAlignedItem>();
foreach (var curmapped in mapped)
{
Progress.Increment(1);
Dictionary <char, List <SAMAlignedLocation> > curMatchedMap;
if (!chrStrandMatchedMap.TryGetValue(curmapped.Seqname, out curMatchedMap))
{
continue;
}
//mapped query must have same oritation with miRNA defined at gff or bed file.
var matches = curMatchedMap[curmapped.Strand];
foreach (var m in matches)
{
if (!curmapped.Overlap(m, 0))
{
continue;
}
var fsl = new FeatureSamLocation(curmapped);
fsl.SamLocation = m;
}
}
}
private void DoMapReadToSequenceRegionOrientationFree(List <FeatureLocation> mapped, List <SAMAlignedItem> reads)
{
//build chr/samlist map
Progress.SetMessage("building chr/samlist map ...");
var chrStrandMatchedMap = new Dictionary <string, List <SAMAlignedLocation> >();
foreach (var read in reads)
{
foreach (var loc in read.Locations)
{
List <SAMAlignedLocation> map;
if (!chrStrandMatchedMap.TryGetValue(loc.Seqname, out map))
{
map = new List <SAMAlignedLocation>();
chrStrandMatchedMap[loc.Seqname] = map;
}
map.Add(loc);
}
}
Progress.SetRange(0, mapped.Count);
var gmapped = new Dictionary <string, SAMAlignedItem>();
foreach (var curmapped in mapped)
{
Progress.Increment(1);
List <SAMAlignedLocation> matches;
if (!chrStrandMatchedMap.TryGetValue(curmapped.Seqname, out matches))
{
continue;
}
foreach (var m in matches)
{
var op = curmapped.OverlapPercentage(m);
if (op < options.MinimumOverlapPercentage)
{
continue;
}
var fsl = new FeatureSamLocation(curmapped);
fsl.SamLocation = m;
}
}
}
public override bool AcceptLocus(SAMAlignedLocation loc)
{
var result = false;
if (!loc.Seqname.Equals(lastSeqname))
{
if (!featureMap.TryGetValue(loc.Seqname, out lastFeatures))
{
return(false);
}
lastSeqname = loc.Seqname;
}
foreach (var feature in lastFeatures)
{
if (feature.End < loc.Start)
{
continue;
}
if (feature.Start > loc.End)
{
break;
}
if (feature.Overlap(loc, this.minOverlapPercentage))
{
result = true;
var samloc = new FeatureSamLocation(feature);
samloc.SamLocation = loc;
feature.SamLocations.Add(samloc);
}
}
return(result);
}
