public void Compare()
{
var collapser = new VariantCollapser(null);
// priority should be given to known, fully anchored, longer, more frequent, and left positioned
var candidateA = GetBasicInsertion();
var candidateB = GetBasicInsertion();
candidateA.OpenOnLeft = true;
candidateB.OpenOnLeft = true;
Assert.Equal(0, collapser.Compare(candidateA, candidateB));
Assert.Equal(0, collapser.Compare(candidateB, candidateA));
candidateA.Alternate = "AAGTACGT";
Assert.Equal(-1, collapser.Compare(candidateA, candidateB));
candidateB.Coordinate = 4;
Assert.Equal(1, collapser.Compare(candidateA, candidateB));
candidateA.Frequency = 0.0000005f;
candidateB.Frequency = 0.0000004f;
Assert.Equal(-1, collapser.Compare(candidateA, candidateB));
candidateB.Alternate = "ACGTACGTT";
Assert.Equal(1, collapser.Compare(candidateA, candidateB));
candidateA.OpenOnLeft = false;
Assert.Equal(-1, collapser.Compare(candidateA, candidateB));
candidateB.IsKnown = true;
Assert.Equal(1, collapser.Compare(candidateA, candidateB));
}
private void ExecuteTest(List <CandidateAllele> candidates, int expectedNumAfter, int?expectedSupport = null, int?maxClearedPosition = null, List <CandidateAllele> known = null,
Action <List <CandidateAllele> > candidateAssertions = null, Action <List <CandidateAllele> > stage = null, Action <List <CandidateAllele> > addedBackAssertions = null)
{
var addedBack = new List <CandidateAllele>();
ResetSupport(candidates);
var collapser = new VariantCollapser(known);
var mockSource = GetMockSource(addedBack);
if (stage != null)
{
stage(candidates);
}
var result = collapser.Collapse(new List <CandidateAllele>(candidates.Select(c => c.DeepCopy())), mockSource.Object, maxClearedPosition);
Assert.Equal(expectedNumAfter, result.Count);
if (expectedSupport.HasValue)
{
Assert.Equal(expectedSupport, result[0].Support);
}
if (candidateAssertions != null)
{
candidateAssertions(result);
}
if (addedBackAssertions != null)
{
addedBackAssertions(addedBack);
}
// order of candidates shouldnt matter
addedBack.Clear();
ResetSupport(candidates);
if (stage != null)
{
stage(candidates);
}
var reverse = new List <CandidateAllele>(candidates.Select(c => c.DeepCopy()));
reverse.Reverse();
result = collapser.Collapse(reverse, mockSource.Object, maxClearedPosition);
Assert.Equal(expectedNumAfter, result.Count);
if (expectedSupport.HasValue)
{
Assert.Equal(expectedSupport, result[0].Support);
}
if (candidateAssertions != null)
{
candidateAssertions(result);
}
if (addedBackAssertions != null)
{
addedBackAssertions(addedBack);
}
}
private void ExecuteEndednessTest(List <CandidateAllele> candidates, bool expectOpenOnLeft, bool expectOpenOnRight)
{
var collapser = new VariantCollapser(null);
var mockSource = GetMockSource(null);
var forward = candidates.Select(candidate => candidate.DeepCopy()).ToList();
var result = collapser.Collapse(forward, mockSource.Object, null);
Assert.Equal(result[0].OpenOnLeft, expectOpenOnLeft);
Assert.Equal(result[0].OpenOnRight, expectOpenOnRight);
}