public void AddReadSummary(int position, ReadCoverageSummary summary)
{
if (IsPositionInRegion(position))
{
var list = _coverageSummaries[position - StartPosition];
if (list == null)
{
_coverageSummaries[position - StartPosition] = new List <ReadCoverageSummary> {
summary
};
}
else
{
list.Add(summary);
}
}
}
public void AddReadSummary(int position, ReadCoverageSummary summary)
{
if (IsPositionInRegion(position))
{
var list = _coverageSummaries[position - StartPosition];
if (list == null)
{
_coverageSummaries[position - StartPosition] = new List <ReadCoverageSummary> {
summary
};
}
else
{
list.Add(summary);
}
}
/// <summary>
/// Returns the index where the Amnplicon name/coverage data is stored.
/// Returns -1 if not found
///
}
private void ExecuteTest(AlleleCategory variantType, DirectionType?expectedDirection, ReadCoverageSummary readSummary,
int variantPosition = 10)
{
var calculator = new ExactCoverageCalculator();
var allele = new CalledAllele(variantType)
{
Coordinate = variantPosition
};
switch (allele.Type)
{
case AlleleCategory.Insertion:
allele.Reference = "A";
allele.Alternate = "ATTTT";
break;
case AlleleCategory.Deletion:
allele.Alternate = "A";
allele.Reference = "ATTTT";
break;
default:
allele.Reference = "AAAA";
allele.Alternate = "TTTT";
break;
}
var source = new Mock <IAlleleSource>();
source.Setup(s => s.GetSpanningReadSummaries(It.IsAny <int>(), It.IsAny <int>()))
.Returns(new List <ReadCoverageSummary> {
readSummary
});
calculator.Compute(allele, source.Object);
for (var i = 0; i < allele.EstimatedCoverageByDirection.Length; i++)
{
Assert.Equal(expectedDirection.HasValue && i == (int)expectedDirection ? 1 : 0, allele.EstimatedCoverageByDirection[i]);
}
}
public void MNV()
{
// full span
// Ref -----mmmm---
// fssssssrr (stitched both sides - should be stitched)
// fsrrrrrrr (stitched on one side - should be reverse)
// fssrrrrrr (partial stitch span - should be stitched)
// ffffffsrr (stitched on one side - should be forward)
// fffffssrr (partial stitch span - should be stitched)
var readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 8,
ClipAdjustedEndPosition = 16,
CigarString = "9M",
DirectionString = "1F:6S:2R"
};
ExecuteTest(AlleleCategory.Mnv, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "1F:1S:7R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Reverse, readSummary);
readSummary.DirectionString = "1F:2S:6R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "6F:1S:2R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Forward, readSummary);
readSummary.DirectionString = "5F:2S:2R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Stitched, readSummary);
// non spanning
// Ref -------mmmm-------
// sssss (should not contribute)
// sssss (should not contribute)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 5,
ClipAdjustedEndPosition = 9,
CigarString = "5M",
DirectionString = "5S"
};
ExecuteTest(AlleleCategory.Mnv, null, readSummary);
readSummary.ClipAdjustedStartPosition = 14;
readSummary.ClipAdjustedEndPosition = 18;
ExecuteTest(AlleleCategory.Mnv, null, readSummary);
// partial span
// Ref -------mmmm-------
// fffss (stitched)
// ffssr (reverse)
// fssrr (forward)
// sssrr (stitched)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 10,
CigarString = "5M",
DirectionString = "3F:2S"
};
ExecuteTest(AlleleCategory.Mnv, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "2F:2S:1R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Reverse, readSummary);
readSummary.ClipAdjustedStartPosition = 13;
readSummary.ClipAdjustedEndPosition = 17;
readSummary.DirectionString = "1F:2S:2R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Forward, readSummary);
readSummary.DirectionString = "3S:2R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Stitched, readSummary);
// partial span with softclipping (capital letter = clipped)
// Ref -------mmmm-------
// fsSSSS (stitched both sides - stitched)
// ffFSRR (forward)
// ffSRRR (forward - this is a tricky one but i think still calling forward is right)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 8,
ClipAdjustedEndPosition = 13,
CigarString = "2M4S",
DirectionString = "1F:5S"
};
ExecuteTest(AlleleCategory.Mnv, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "3F:1S:2R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Forward, readSummary);
readSummary.DirectionString = "2F:1S:3R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Forward, readSummary);
// other mutant?
// Ref -----++mmmm-------
// fs-----sssrr (deletion right next to it - stitched)
// fs--------rr (fully spanning deletion - reverse)
// fs--------sr (fully spanning deletion - stitched)
// fffff----ssr (insertion next to deletion - forward)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 7,
ClipAdjustedEndPosition = 16,
CigarString = "2M3D5M",
DirectionString = "1F:4S:2R"
};
ExecuteTest(AlleleCategory.Mnv, DirectionType.Stitched, readSummary);
readSummary.CigarString = "2M6D2M";
readSummary.DirectionString = "1F:1S:2R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Reverse, readSummary);
readSummary.DirectionString = "1F:2S:1R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Stitched, readSummary);
readSummary.CigarString = "5M4D3M";
readSummary.DirectionString = "5F:2S:1R";
ExecuteTest(AlleleCategory.Mnv, DirectionType.Forward, readSummary);
}
public void Insertion()
{
// wildtype full span
// Ref -------++++-------
// ffsss ssrr (stitched both sides - should be stitched)
// ffsss rrrr (stitched on one side - should be reverse)
// fffff ssrr (stitched on one side - should be forward)
var readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 14,
Cigar = new CigarAlignment("9M"),
DirectionString = "2F:5S:2R"
};
ExecuteTest(AlleleCategory.Insertion, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "2F:3S:4R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Reverse, readSummary);
readSummary.DirectionString = "5F:2S:2R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Forward, readSummary);
// non spanning
// Ref -------++++-------
// sssss (should not contribute)
// sssss (should not contribute)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 10,
CigarString = "5M",
DirectionString = "5S"
};
ExecuteTest(AlleleCategory.Insertion, null, readSummary);
readSummary.ClipAdjustedStartPosition = 11;
readSummary.ClipAdjustedEndPosition = 15;
ExecuteTest(AlleleCategory.Insertion, null, readSummary);
// mutant full span
// Ref -------++++-------
// ffsssssssssrr (stitched both sides - should be stitched)
// ffsssrrrrrrrr (stitched on one side - should be reverse)
// fffffffffssrr (stitched on one side - should be forward)
// ffffffffsssrr (partial stitched - should be stitched)
// ffssssrrrrrrr (partial stitched - should be stitched)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 14,
CigarString = "5M4I4M",
DirectionString = "2F:9S:2R"
};
ExecuteTest(AlleleCategory.Insertion, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "2F:3S:8R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Reverse, readSummary);
readSummary.DirectionString = "9F:2S:2R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Forward, readSummary);
readSummary.DirectionString = "8F:3S:2R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "2F:4S:7R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Stitched, readSummary);
// mutant partial or exact span
// Ref -------++++-------
// ffssssrrr (partial stitched - should be stitched)
// ffsssr (partial span - stitched on one side - should be reverse)
// fffsssrr (partial stitched - should be stitched)
// ffssrr (partial span - stitched on one side - should be reverse)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 10,
CigarString = "5M4I",
DirectionString = "2F:4S:3R"
};
ExecuteTest(AlleleCategory.Insertion, DirectionType.Stitched, readSummary);
readSummary.CigarString = "5M1I";
readSummary.DirectionString = "2F:3S:1R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Reverse, readSummary);
readSummary.ClipAdjustedStartPosition = 11;
readSummary.ClipAdjustedEndPosition = 14;
readSummary.CigarString = "4I4M";
readSummary.DirectionString = "2F:2S:2R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Stitched, readSummary);
readSummary.CigarString = "2I4M";
readSummary.DirectionString = "2F:3S:1R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Forward, readSummary);
// other mutant?
// Ref -------++++-------
// ffs---sssssrr (deletion next to insertion of diff length?)
// ffs---rrrrrrr (deletion next to insertion of diff length?)
// ffsss-----rrr (deletion next to insertion of diff length?)
// ffs-------srr (big deletion)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 14,
CigarString = "3M3D7M",
DirectionString = "2F:6S:2R"
};
ExecuteTest(AlleleCategory.Insertion, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "2F:1S:7R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Reverse, readSummary);
readSummary.CigarString = "5M1D3M";
readSummary.DirectionString = "2F:3S:3R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Reverse, readSummary);
readSummary.CigarString = "3M3D3M";
readSummary.DirectionString = "2F:2S:2R";
ExecuteTest(AlleleCategory.Insertion, DirectionType.Stitched, readSummary);
}
public void Deletion()
{
// wildtype full span
// Ref -----dddd-------
// ffssssssrr (stitched both sides - should be stitched)
// ffsrrrrrrr (stitched on one side - should be reverse)
// ffssrrrrrr (partial stitch span - should be stitched)
// fffffffsrr (stitched on one side - should be forward)
// ffffffssrr (partial stitch span - should be stitched)
var readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 8,
ClipAdjustedEndPosition = 13,
CigarString = "10M",
DirectionString = "2F:6S:2R"
};
ExecuteTest(AlleleCategory.Deletion, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "2F:1S:7R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Reverse, readSummary);
readSummary.DirectionString = "2F:2S:6R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "7F:1S:2R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Forward, readSummary);
readSummary.DirectionString = "6F:2S:2R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Stitched, readSummary);
// non spanning
// Ref -------dddd-------
// sssss (should not contribute)
// sssss (should not contribute)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 10,
CigarString = "5M",
DirectionString = "5S"
};
ExecuteTest(AlleleCategory.Deletion, null, readSummary);
readSummary.ClipAdjustedStartPosition = 15;
readSummary.ClipAdjustedEndPosition = 19;
ExecuteTest(AlleleCategory.Deletion, null, readSummary);
// mutant full span
// Ref -------dddd-------
// ffffs----srrr (stitched both sides - should be stitched)
// ffsss----rrrr (stitched on one side - should be reverse)
// fffff----ssrr (stitched on one side - should be forward)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 18,
CigarString = "5M4D4M",
DirectionString = "4F:2S:3R"
};
ExecuteTest(AlleleCategory.Deletion, DirectionType.Stitched, readSummary);
readSummary.DirectionString = "2F:3S:4R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Reverse, readSummary);
readSummary.DirectionString = "5F:2S:2R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Forward, readSummary);
// mutant partial span (capital letter = clipped)
// note deletions can only be observed if there is soft clipping after
// Ref -------dddd-------
// ffffs----SSSS (stitched both sides - stitched)
// fffff---FSRR (forward)
// fffff---SRRR (forward - this is a tricky one but i think still calling forward is right)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 6,
ClipAdjustedEndPosition = 18,
CigarString = "5M4D4S",
DirectionString = "4F:5S"
};
ExecuteTest(AlleleCategory.Deletion, DirectionType.Stitched, readSummary);
readSummary.CigarString = "5M3D5S";
readSummary.DirectionString = "6F:1S:2R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Forward, readSummary);
readSummary.DirectionString = "5F:1S:3R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Forward, readSummary);
// other mutant?
// Ref -----++dddd-------
// fs-----sssrr (another deletion right next to it - stitched)
// fs--------rr (bigger deletion spanning - reverse)
// fs--------sr (bigger deletion spanning - stitched)
// fffff----ssr (insertion next to deletion - forward)
readSummary = new ReadCoverageSummary
{
ClipAdjustedStartPosition = 8,
ClipAdjustedEndPosition = 17,
CigarString = "2M3D5M",
DirectionString = "1F:4S:2R"
};
ExecuteTest(AlleleCategory.Deletion, DirectionType.Stitched, readSummary);
readSummary.CigarString = "2M6D2M";
readSummary.DirectionString = "1F:1S:2R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Reverse, readSummary);
readSummary.DirectionString = "1F:2S:1R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Stitched, readSummary);
readSummary.CigarString = "5M4D3M";
readSummary.DirectionString = "5F:2S:1R";
ExecuteTest(AlleleCategory.Deletion, DirectionType.Forward, readSummary);
}