public void GetFirstVariantPosition_multi_chrom_index()
{
var index = new JasixIndex();
index.Add("chr1", 100, 101, 100000);
index.Add("chr1", 105, 109, 100050);
index.Add("chr1", 160, 166, 100100);
index.Add("chr2", 100, 100, 100150);
index.Add("chr2", 102, 105, 100200);
index.Flush();
var chrPos = Utilities.ParseQuery("chr1");
Assert.Equal(100000, index.GetFirstVariantPosition(chrPos.Item1, chrPos.Item2, chrPos.Item3));
chrPos = Utilities.ParseQuery("chr2");
Assert.Equal(100150, index.GetFirstVariantPosition(chrPos.Item1, chrPos.Item2, chrPos.Item3));
}
public void FindLargeVaritants_method_does_not_return_small_variants()
{
var index = new JasixIndex();
index.Add("chr1", 100, 101, 100_000);
index.Add("chr1", 105, 109, 100_050);
index.Add("chr1", 160, 166, 100_100);
index.Add("chr1", 200, 1000, 100_075);//large variant
index.Add("chr2", 100, 100, 100_150);
index.Add("chr2", 102, 105, 100_200);
index.Flush();
//checking large variants
Assert.Null(index.LargeVariantPositions("chr1", 100, 199));
var largeVariants = index.LargeVariantPositions("chr1", 100, 201);
Assert.NotNull(largeVariants);
Assert.Single(largeVariants);
Assert.Equal(100075, largeVariants[0]);
}
public void Add_fill_node_and_start_another()
{
var index = new JasixIndex();
//creating two nodes each containing 50 entries
for (var i = 0; i < 2 * JasixCommons.PreferredNodeCount; i++)
{
index.Add("chr1", 100 + i, 101 + i, 100_000 + i);
}
index.Add("chr1", 160 + 2 * JasixCommons.PreferredNodeCount, 166 + 2 * JasixCommons.PreferredNodeCount, 200_100);
index.Add("chr2", 100, 100, 200_150);
index.Add("chr2", 102, 105, 200_200);
index.Flush();
Assert.Equal(100_000, index.GetFirstVariantPosition("chr1", 100, 102));
Assert.Equal(100_000 + JasixCommons.PreferredNodeCount, index.GetFirstVariantPosition("chr1", 2 * JasixCommons.PreferredNodeCount + 55, 2 * JasixCommons.PreferredNodeCount + 55));
Assert.Equal(-1, index.GetFirstVariantPosition("chr1", 2 * JasixCommons.PreferredNodeCount + 120, 2 * JasixCommons.PreferredNodeCount + 124));
Assert.Equal(200_100, index.GetFirstVariantPosition("chr1", 2 * JasixCommons.PreferredNodeCount + 158, 2 * JasixCommons.PreferredNodeCount + 160));
Assert.Equal(200_150, index.GetFirstVariantPosition("chr2", 103, 105));
}
public void Combination_of_large_and_small_variants()
{
var index = new JasixIndex();
//query range 10,000- 10,020
index.Add("chr1", 8_000, 9_900, 90_000); //SV not overlapping the query
index.Add("chr1", 9_000, 10_005, 90_100); // partially overlapping
index.Add("chr1", 9_500, 10_050, 90_200); //completely overlapping
index.Add("chr1", 10_000, 10_001, 100_000);
index.Add("chr1", 10_004, 10_006, 100_100);
index.Add("chr1", 10_009, 10_550, 100_200);//SV starting from the middle of the range
index.Add("chr1", 10_008, 10_010, 100_300);
index.Add("chr1", 10_011, 10_020, 100_400);
index.Add("chr1", 10_039, 10_550, 100_200);//SV past the range
index.Flush();
var firstSmallVarLocation = index.GetFirstVariantPosition("chr1", 10_000, 10_020);
var largeVariantLocations = index.LargeVariantPositions("chr1", 10_000, 10_020);
Assert.Equal(90_000, firstSmallVarLocation);
Assert.True(largeVariantLocations.SequenceEqual(new List <long> {
90_100, 90_200, 100_200
}));