public void GetEmptySummaryForAmpliconTest()
{
AmpliconCounts exampleCounts = AmpliconCounts.GetEmptyAmpliconCounts();
Assert.Equal(Constants.MaxNumOverlappingAmplicons, exampleCounts.AmpliconNames.Length);
Assert.Equal(Constants.MaxNumOverlappingAmplicons, exampleCounts.CountsForAmplicon.Length);
Assert.Equal(0, exampleCounts.GetCountsForAmplicon("amp1"));
Assert.Equal(0, exampleCounts.GetCountsForAmplicon("amp2"));
Assert.Equal(0, exampleCounts.GetCountsForAmplicon("amp3"));
Assert.Equal(0, exampleCounts.GetCountsForAmplicon(""));
Assert.Equal(0, exampleCounts.GetCountsForAmplicon("foo"));
}
private static void SetAmpliconName(bool trackAmpliconCounts, Read alignment, CandidateAllele variant)
{
if (!trackAmpliconCounts)
{
return;
}
var ampliconName = alignment.GetAmpliconNameIfExists();
if (ampliconName != null)
{
var summary = AmpliconCounts.GetEmptyAmpliconCounts();
summary.AmpliconNames[0] = ampliconName;
summary.CountsForAmplicon[0] = 1;
variant.SupportByAmplicon = summary;
}
}
public void AddSupport(CandidateAllele fromAllele)
{
for (var i = 0; i < SupportByDirection.Length; i++)
{
SupportByDirection[i] += fromAllele.SupportByDirection[i];
}
for (var i = 0; i < WellAnchoredSupportByDirection.Length; i++)
{
WellAnchoredSupportByDirection[i] += fromAllele.WellAnchoredSupportByDirection[i];
}
if (fromAllele.SupportByAmplicon.AmpliconNames != null && fromAllele.SupportByAmplicon.AmpliconNames.Length > 0)
{
if (SupportByAmplicon.AmpliconNames == null || SupportByAmplicon.AmpliconNames.Length == 0)
{
SupportByAmplicon = AmpliconCounts.GetEmptyAmpliconCounts();
}
for (var i = 0; i < fromAllele.SupportByAmplicon.AmpliconNames.Length; i++)
{
var fromAlleleCount = fromAllele.SupportByAmplicon.CountsForAmplicon[i];
var fromAlleleName = fromAllele.SupportByAmplicon.AmpliconNames[i];
var indexData = SupportByAmplicon.GetAmpliconNameIndex(fromAlleleName);
if (indexData.IndexForAmplicon > -1)
{
SupportByAmplicon.CountsForAmplicon[indexData.IndexForAmplicon] += fromAlleleCount;
}
else
{
SupportByAmplicon.AmpliconNames[indexData.NextOpenSlot] = fromAlleleName;
SupportByAmplicon.CountsForAmplicon[indexData.NextOpenSlot] += fromAlleleCount;
}
}
}
}
public void AddCandidate(CandidateAllele newCandidate, bool trackOpenEnded, bool trackAmplicon)
{
if (newCandidate.Type == AlleleCategory.Reference)
{
throw new ArgumentException(string.Format("Unable to add candidate '{0}': reference candidates are not tracked.", newCandidate));
}
if (!IsPositionInRegion(newCandidate.ReferencePosition))
{
throw new ArgumentException(string.Format("Unable to add candidate at position {0} to region '{1}'",
newCandidate.ReferencePosition, Name));
}
var regionIndex = newCandidate.ReferencePosition - StartPosition;
var existingCandidates = _candidateVariantsLookup[regionIndex];
if (existingCandidates == null)
{
_candidateVariantsLookup[regionIndex] = new List <CandidateAllele> {
newCandidate
}
}
;
else
{
//TJD - this used to be a hash table, not a find,
//where each variants unique signature was the key.
//this might be why we have seen a performance hit in the new pisces.
var foundAtIndex = trackOpenEnded ?
existingCandidates.FindIndex(c => c.Equals(newCandidate) &&
c.OpenOnLeft == newCandidate.OpenOnLeft &&
c.OpenOnRight == newCandidate.OpenOnRight) :
existingCandidates.FindIndex(c => c.Equals(newCandidate));
if (foundAtIndex == -1)
{
existingCandidates.Add(newCandidate);
}
else
{
var existingMatch = existingCandidates[foundAtIndex];
for (var i = 0; i < existingMatch.SupportByDirection.Length; i++)
{
existingMatch.SupportByDirection[i] += newCandidate.SupportByDirection[i];
}
for (var i = 0; i < existingMatch.WellAnchoredSupportByDirection.Length; i++)
{
existingMatch.WellAnchoredSupportByDirection[i] += newCandidate.WellAnchoredSupportByDirection[i];
}
for (var i = 0; i < existingMatch.ReadCollapsedCountsMut.Length; i++)
{
existingMatch.ReadCollapsedCountsMut[i] += newCandidate.ReadCollapsedCountsMut[i];
}
if ((trackAmplicon) && (newCandidate.SupportByAmplicon.AmpliconNames != null))
{
string[] ampliconList = newCandidate.SupportByAmplicon.AmpliconNames;
for (var i = 0; i < ampliconList.Length; i++)
{
var ampliconName = ampliconList[i];
if (ampliconName == null)
{
continue;
}
if (existingMatch.SupportByAmplicon.AmpliconNames == null || existingMatch.SupportByAmplicon.AmpliconNames.Length == 0)
{
existingMatch.SupportByAmplicon = AmpliconCounts.GetEmptyAmpliconCounts();
}
var existingAmpliconIndexData = existingMatch.SupportByAmplicon.GetAmpliconNameIndex(ampliconName);
var ampliconIndex = existingAmpliconIndexData.IndexForAmplicon;
var availableSlot = existingAmpliconIndexData.NextOpenSlot;
if (ampliconIndex == -1)
{
existingMatch.SupportByAmplicon.AmpliconNames[availableSlot] = ampliconName;
existingMatch.SupportByAmplicon.CountsForAmplicon[availableSlot] = 1;
}
else
{
existingMatch.SupportByAmplicon.AmpliconNames[ampliconIndex] = ampliconName;
existingMatch.SupportByAmplicon.CountsForAmplicon[ampliconIndex]++;
}
}
}
}
}
UpdateMaxPosition(newCandidate);
}