public void DoneProcessing()
{
var stateManager = new RealignStateManager();
var allCandidates = new List <CandidateIndel>
{
new CandidateIndel(new CandidateAllele("chr1", 500, "A", "AT", AlleleCategory.Insertion)),
new CandidateIndel(new CandidateAllele("chr1", 1500, "A", "AT", AlleleCategory.Insertion)),
new CandidateIndel(new CandidateAllele("chr1", 3000, "A", "AT", AlleleCategory.Insertion)),
new CandidateIndel(new CandidateAllele("chr1", 4000, "A", "AT", AlleleCategory.Insertion)),
new CandidateIndel(new CandidateAllele("chr1", 4010, "A", "AT", AlleleCategory.Insertion))
};
stateManager.AddCandidates(allCandidates);
var batch = stateManager.GetCandidatesToProcess(1);
Assert.Equal(null, batch.ClearedRegions);
Assert.False(batch.HasCandidates);
stateManager.DoneProcessing(batch); // effectively does nothing
// candidates from all previous blocks but nothing cleared
batch = stateManager.GetCandidatesToProcess(2001);
Assert.Equal(1, batch.ClearedRegions.Count);
Assert.Equal(1000, batch.ClearedRegions[0].EndPosition);
stateManager.DoneProcessing(batch); // clear first block, but keep it's candidates
batch = stateManager.GetCandidatesToProcess(3001);
Assert.Equal(1, batch.ClearedRegions.Count);
Assert.Equal(2000, batch.ClearedRegions[0].EndPosition);
VerifyBatchCandidates(batch, allCandidates.Where(c => c.ReferencePosition == 500 || c.ReferencePosition == 1500 || c.ReferencePosition == 3000).ToList());
stateManager.DoneProcessing(batch); // clear second block, purge block 1 candidates, but keep block 2 candidates
batch = stateManager.GetCandidatesToProcess(4500);
Assert.Equal(1, batch.ClearedRegions.Count);
Assert.Equal(3000, batch.ClearedRegions[0].EndPosition);
VerifyBatchCandidates(batch, allCandidates.Where(c => c.ReferencePosition == 1500 || c.ReferencePosition == 3000 || c.ReferencePosition == 4000).ToList());
}
public void GetCandidates()
{
var stateManager = new RealignStateManager();
var allCandidates = new List <CandidateIndel>
{
new CandidateIndel(new CandidateAllele("chr1", 500, "A", "AT", AlleleCategory.Insertion)),
new CandidateIndel(new CandidateAllele("chr1", 1500, "A", "AT", AlleleCategory.Insertion)),
new CandidateIndel(new CandidateAllele("chr1", 3000, "A", "AT", AlleleCategory.Insertion))
};
stateManager.AddCandidates(allCandidates);
// enforce 1 block window for cleared region
var batch = stateManager.GetCandidatesToProcess(1);
Assert.Equal(null, batch.ClearedRegions);
Assert.False(batch.HasCandidates);
batch = stateManager.GetCandidatesToProcess(501);
Assert.Equal(null, batch);
// candidates from all previous blocks but nothing cleared
batch = stateManager.GetCandidatesToProcess(1999);
Assert.Equal(null, batch.ClearedRegions);
VerifyBatchCandidates(batch, allCandidates.Where(c => c.ReferencePosition == 500).ToList());
batch = stateManager.GetCandidatesToProcess(2001);
Assert.Equal(1, batch.ClearedRegions.Count);
Assert.Equal(1000, batch.ClearedRegions[0].EndPosition);
VerifyBatchCandidates(batch, allCandidates.Where(c => c.ReferencePosition == 500 || c.ReferencePosition == 1500).ToList());
batch = stateManager.GetCandidatesToProcess(4000);
Assert.Equal(2, batch.ClearedRegions.Count);
Assert.Equal(2000, batch.ClearedRegions[1].EndPosition);
VerifyBatchCandidates(batch, allCandidates);
batch = stateManager.GetCandidatesToProcess(null);
Assert.Equal(null, batch.ClearedRegions);
VerifyBatchCandidates(batch, allCandidates);
}
