public void GetPrunedPreIndelsForChromosome_BinFiltering()
{
// 3 indels very close to each other. One has significantly better score.
var preIndelsRaw = new List <PreIndel>()
{
GetIndel(122, "A", "ATG", 5),
GetIndel(123, "A", "ATC", 11),
GetIndel(124, "A", "ATT", 5),
};
var filterer = new IndelPruner(false, 1);
var pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
// Remove the weaker nearby ones, but don't up the score
Assert.Equal(1.0, pruned.Count);
Assert.Equal(preIndelsRaw[1], pruned[0]);
Assert.Equal(11, pruned[0].Score);
// Nearby weak indel is longer than the strong one. Don't remove the weak one as it may have just been harder to call than the smaller one.
preIndelsRaw = new List <PreIndel>()
{
GetIndel(122, "A", "ATGA", 5),
GetIndel(123, "A", "ATC", 11),
GetIndel(124, "A", "ATT", 5),
};
pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(2, pruned.Count);
// One is not significantly better than the rest. Keep all.
preIndelsRaw = new List <PreIndel>()
{
GetIndel(122, "A", "ATG", 5),
GetIndel(123, "A", "ATC", 10),
GetIndel(124, "A", "ATT", 5),
};
pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(3, pruned.Count);
// One is not significantly better than the rest. Keep all.
preIndelsRaw = new List <PreIndel>()
{
GetIndel(122, "A", "ATG", 5),
GetIndel(123, "A", "ATC", 10),
GetIndel(124, "A", "ATT", 5),
GetIndel(125, "A", "ATTG", 5),
};
pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(4, pruned.Count);
// 3 indels very close to each other. One has significantly better score
// Get rid of the other nearby ones, but keep the one that is not within the bin
preIndelsRaw = new List <PreIndel>()
{
GetIndel(122, "A", "ATG", 5),
GetIndel(123, "A", "ATC", 11),
GetIndel(124, "A", "ATT", 5),
GetIndel(125, "A", "ATTG", 5),
};
pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(2, pruned.Count);
}
public void GetPrunedPreIndelsForChromosome_ConcurrentIndels()
{
// 3 small indels, same position, same score
var preIndelsRaw = new List <PreIndel>()
{
GetIndel(123, "A", "ATC", 5),
GetIndel(123, "A", "ATG", 5),
GetIndel(123, "A", "ATT", 5),
};
var filterer = new IndelPruner(false, 0);
var pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(3, pruned.Count);
// 3 long concurrent insertions, one has a better score than the others. take that one, and up the score
preIndelsRaw = new List <PreIndel>()
{
GetIndel(123, "A", "ATCGTTGTTGT", 6),
GetIndel(123, "A", "ATCTTTGTTGT", 5),
GetIndel(123, "A", "ATTGTTGTTGT", 5),
};
pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(1.0, pruned.Count);
Assert.Equal(preIndelsRaw[0], pruned[0]);
Assert.Equal(11, pruned[0].Score);
// 3 long concurrent insertions, same score... can't choose a best one
preIndelsRaw = new List <PreIndel>()
{
GetIndel(123, "A", "ATCGTTGTTGT", 5),
GetIndel(123, "A", "ATCGTTGTTGT", 5),
GetIndel(123, "A", "ATTGTTGTTGT", 5),
};
pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(3, pruned.Count);
// 3 long concurrent insertions, two have the same high score... can't choose a best one
preIndelsRaw = new List <PreIndel>()
{
GetIndel(123, "A", "ATCGTTGTTGT", 10),
GetIndel(123, "A", "ATCGTTGTTGT", 10),
GetIndel(123, "A", "ATTGTTGTTGT", 5),
};
pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(3, pruned.Count);
// 3 shorter concurrent insertions, different scores, would have been able to choose a best one
// but they're too short to fall under concurrent insertions (>=10bp), and we're not doing bin filtering
preIndelsRaw = new List <PreIndel>()
{
GetIndel(123, "A", "ATCGTTGTTG", 5),
GetIndel(123, "A", "ATCGTTGTTG", 5),
GetIndel(123, "A", "ATTGTTGTTG", 5),
};
pruned = filterer.GetPrunedPreIndelsForChromosome(preIndelsRaw);
Assert.Equal(3, pruned.Count);
}