private static void AddMultiIndelMetrics(IndelEvidence indelMetrics, List <PreIndel> indels, int totalNm)
{
indelMetrics.LeftAnchor += indels[0].LeftAnchor;
indelMetrics.RightAnchor += indels[1].RightAnchor;
indelMetrics.Mess += Math.Max(0, totalNm - indels.Sum(x => x.Length));
indelMetrics.Quality += indels.Min(x => x.AverageQualityRounded);
}
private static void AddIndelMetrics(IndelEvidence indelMetrics, PreIndel indel, int totalNm)
{
indelMetrics.Position = indel.ReferencePosition;
indelMetrics.LeftAnchor += indel.LeftAnchor;
indelMetrics.RightAnchor += indel.RightAnchor;
indelMetrics.Mess += Math.Max(0, totalNm - indel.Length);
indelMetrics.Quality += indel.AverageQualityRounded;
}
private static IndelEvidence IndelMetrics(Dictionary <string, IndelEvidence> lookup, string indelKey)
{
if (!lookup.TryGetValue(indelKey, out var indelMetrics))
{
//indelMetrics = new int[11];
indelMetrics = new IndelEvidence();
lookup.Add(indelKey, indelMetrics);
}
return(indelMetrics);
}
public int Position; // TODO this is the wrong place for this but i need it for now
public void AddIndelEvidence(IndelEvidence other)
{
Stitched += other.Stitched;
Forward += other.Forward;
Reverse += other.Reverse;
Observations += other.Observations;
Quality += other.Quality;
Mess += other.Mess;
LeftAnchor += other.LeftAnchor;
RightAnchor += other.RightAnchor;
IsRepeat += other.IsRepeat;
ReputableSupport += other.ReputableSupport;
IsSplit += other.IsSplit;
Position = other.Position;
}
private static void AddReadLevelIndelMetrics(BamAlignment bamAlignment, bool isReputable, bool stitched, IndelEvidence indelMetrics,
bool isRepeat)
{
indelMetrics.Observations++;
if (stitched)
{
indelMetrics.Stitched++;
}
else
{
if (bamAlignment.IsReverseStrand())
{
indelMetrics.Reverse++;
}
else
{
indelMetrics.Forward++;
}
}
if (isReputable)
{
indelMetrics.ReputableSupport++;
}
if (isRepeat)
{
indelMetrics.IsRepeat++;
}
if (!bamAlignment.IsMateMapped() || bamAlignment.MateRefID != bamAlignment.RefID)
{
indelMetrics.IsSplit++;
}
}
private static void UpdateIndelMetrics(BamAlignment bamAlignment, bool isReputable, bool stitched, IndelEvidence indelMetrics,
PreIndel indel, int totalNm)
{
// TODO - are read-level repeats that informative? Because this is kind of a perf burden
// (^ Removed for now for that reason)
bool isRepeat = false;
//var isRepeat = StitchingLogic.OverlapEvaluator.IsRepeat(bamAlignment.Bases.Substring(0, (int)indel.LeftAnchor), 2, out repeatUnit) || StitchingLogic.OverlapEvaluator.IsRepeat(bamAlignment.Bases.Substring(0, (int)indel.RightAnchor), 2, out repeatUnit);
AddReadLevelIndelMetrics(bamAlignment, isReputable, stitched, indelMetrics, isRepeat);
AddIndelMetrics(indelMetrics, indel, totalNm);
}
