public void AddAndGetCandidates_Errors()
{
var testRegion = new MyRegionState(1000, 2000);
Assert.Throws <ArgumentException>(
() => testRegion.AddCandidate(new CandidateAllele("chr1", 999, "A", "T", AlleleCategory.Snv)));
Assert.Throws <ArgumentException>(
() => testRegion.GetAlleleCount(2001, AlleleType.A, DirectionType.Forward));
}
public void AddAndGetCandidates()
{
// -----------------------------------------------
// simple test case adding candidate to empty region
// -----------------------------------------------
var testRegion = new MyRegionState(1000, 2000);
var snv1 = new CandidateAllele("chr1", 1500, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 10, 0, 0 }
};
testRegion.AddCandidate(snv1);
var allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 1);
var fetchedCandidate = allCandidates[0];
Assert.True(fetchedCandidate.Equals(snv1));
// -----------------------------------------------
// add same type of candidate but at different position
// -----------------------------------------------
var snv2 = new CandidateAllele("chr1", 1501, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(snv2);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 2);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 10);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
// -----------------------------------------------
// add a different type of candidate at same position
// -----------------------------------------------
var deletion1 = new CandidateAllele("chr1", 1500, "AT", "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 15, 0, 0 }
};
testRegion.AddCandidate(deletion1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 10);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 15);
// -----------------------------------------------
// add same variant, but more coverage
// -----------------------------------------------
var moreSnv1 = new CandidateAllele("chr1", 1500, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 2, 0, 0 }, ReadCollapsedCountsMut = new[] { 9, 8, 7, 6, 0, 0, 0, 0 }
};
testRegion.AddCandidate(moreSnv1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is incremented, read counts incremented
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 12);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCountsMut[i] == moreSnv1.ReadCollapsedCountsMut[i]);
}
// make sure coverage is preserved, read counts preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCountsMut[i] == 0);
}
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 15);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCountsMut[i] == 0);
}
var moreDeletion1 = new CandidateAllele("chr1", 1500, "AT", "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 0, 18, 0 }
};
testRegion.AddCandidate(moreDeletion1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is incremented
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 33);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 12);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
// -----------------------------------------------
// add insertion that goes off block
// -----------------------------------------------
var edgeInsertion = new CandidateAllele("chr1", 2000, "A", "TCG", AlleleCategory.Insertion)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeInsertion);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 4);
Assert.Equal(2001, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add mnv that goes off block
// -----------------------------------------------
var edgeMnv = new CandidateAllele("chr1", 1999, "ATCC", "TCGG", AlleleCategory.Mnv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeMnv);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 5);
Assert.Equal(2002, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add deletion that goes off block
// -----------------------------------------------
var edgeDeletion = new CandidateAllele("chr1", 1999, "A" + new string('T', 25), "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeDeletion);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 6);
Assert.Equal(2025, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add variant that goes off block but not as far as the deletion did - max endpoint should stay the same
// -----------------------------------------------
var edgeMnv2 = new CandidateAllele("chr1", 1999, "ATCGA", "TCGCT", AlleleCategory.Mnv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeMnv2);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 7);
Assert.Equal(2025, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add candidate group
// -----------------------------------------------
var candidateGroupAdd1 = new List <CandidateAllele>()
{
snv1, snv2
};
var candidateGroupAdd2 = new List <CandidateAllele>()
{
deletion1, edgeDeletion
};
var candidateGroupAdd3 = new List <CandidateAllele>()
{
edgeMnv, edgeInsertion, snv1
};
var candidateGroupAdd4 = new List <CandidateAllele>()
{
moreSnv1
};
// candidateGroupAdd5 has the same variants as candidateGroupAdd1. should not generate a new group
var snv1Duplicate = new CandidateAllele("chr1", 1500, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 10, 0, 0 }
};
var candidateGroupAdd5 = new List <CandidateAllele>()
{
snv1Duplicate, snv2
};
var candidateGroupAdd = new List <List <CandidateAllele> >()
{
candidateGroupAdd1, candidateGroupAdd2, candidateGroupAdd3, candidateGroupAdd4, candidateGroupAdd5
};
foreach (var candidate in candidateGroupAdd)
{
testRegion.AddCandidateGroup(candidate);
}
testRegion.AddCandidateGroup(candidateGroupAdd1);
var candidateGroupGet = testRegion.GetBlockCandidateGroup();
Assert.Equal(candidateGroupGet.Count, 5);
Assert.True(candidateGroupGet.Contains(new Tuple <string, string, string>(snv1.ToString(), snv2.ToString(), null)));
Assert.False(candidateGroupGet.Contains(new Tuple <string, string, string>(snv2.ToString(), snv1.ToString(), null)));
Assert.True(candidateGroupGet.Contains(new Tuple <string, string, string>(deletion1.ToString(), edgeDeletion.ToString(), null)));
Assert.True(candidateGroupGet.Contains(new Tuple <string, string, string>(snv1.ToString(), edgeMnv.ToString(), edgeInsertion.ToString())));
Assert.True(candidateGroupGet.Contains(new Tuple <string, string, string>(snv1.ToString(), edgeMnv.ToString(), null)));
Assert.True(candidateGroupGet.Contains(new Tuple <string, string, string>(edgeMnv.ToString(), edgeInsertion.ToString(), null)));
Assert.False(candidateGroupGet.Contains(new Tuple <string, string, string>(edgeMnv.ToString(), snv1.ToString(), edgeInsertion.ToString())));
Assert.False(candidateGroupGet.Contains(new Tuple <string, string, string>(snv1.ToString(), edgeInsertion.ToString(), null)));
}
