public void ShouldSkipReadTest()
{
var nbhdReadFilter = new NeighborhoodReadFilter(new BamFilterParameters()
{
MinimumMapQuality = 20
});
var neighbor1 = new VcfNeighborhood(0, "chr1", new VariantSite(10000), new VariantSite(200000))
{
VcfVariantSites = new List <VariantSite>
{
new VariantSite(10)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "C"
},
new VariantSite(15)
{
VcfReferenceAllele = "G", VcfAlternateAllele = "A"
},
},
};
neighbor1.SetRangeOfInterest();
var callableNeighbor1 = new CallableNeighborhood(neighbor1, new VariantCallingParameters(), null);
var read1 = TestHelper.CreateRead("chr1", "ACGT", 6); // Read ends before first variant
Assert.Equal(true, nbhdReadFilter.ShouldSkipRead(read1, callableNeighbor1));
var read2 = TestHelper.CreateRead("chr1", "ACGT", 7); // Read covers 1 base of the nbhd
Assert.Equal(false, nbhdReadFilter.ShouldSkipRead(read2, callableNeighbor1));
var read3 = TestHelper.CreateRead("chr1", "ACGT", 12); // Read partially covers neighborhood
Assert.Equal(false, nbhdReadFilter.ShouldSkipRead(read3, callableNeighbor1));
var read4 = TestHelper.CreateRead("chr1", "ACGT", 16); // Read starts after neighborhood
Assert.Equal(false, nbhdReadFilter.ShouldSkipRead(read4, callableNeighbor1));
// Nima: we can maybe add features to CreateRead to be able to create PCR duplicate, low mapQ, and non proper pair reads
// but i think these conditions are somewhat trivial, and this may not be necessary.
}
public void ClippedReadCountTest()
{
var neighbor1 = new VcfNeighborhood(0, "chr1", new VariantSite(10000), new VariantSite(200000))
{
VcfVariantSites = new List <VariantSite>
{
new VariantSite(10)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "C"
},
new VariantSite(15)
{
VcfReferenceAllele = "G", VcfAlternateAllele = "A"
},
new VariantSite(25)
{
VcfReferenceAllele = "T", VcfAlternateAllele = "G"
},
},
};
neighbor1.SetRangeOfInterest();
Assert.Equal(9, neighbor1.SoftClipEndBeforeNbhd);
Assert.Equal(26, neighbor1.SoftClipPosAfterNbhd);
var callableNeighbor1 = new CallableNeighborhood(neighbor1, new VariantCallingParameters(), null);
var nbhdReadFilter = new NeighborhoodReadFilter(new BamFilterParameters()
{
MinimumMapQuality = 20
});
var cigarMatch = new CigarAlignment("4M");
var read1 = TestHelper.CreateRead("chr1", "ACGT", 6, cigarMatch); // No clip, ends before neighborhood starts
Assert.Equal(false, nbhdReadFilter.IsClippedWithinNeighborhood(read1, callableNeighbor1));
var read2 = TestHelper.CreateRead("chr1", "ACGT", 8, cigarMatch); // No clip, partially covers neighborhood
Assert.Equal(false, nbhdReadFilter.IsClippedWithinNeighborhood(read2, callableNeighbor1));
var read3 = TestHelper.CreateRead("chr1", "ACGT", 15, cigarMatch); // No clip, inside neighborhood
Assert.Equal(false, nbhdReadFilter.IsClippedWithinNeighborhood(read3, callableNeighbor1));
// Clipped portion of read starts before neighborhood -> NOT within neighborhood
// POS 8 9 10 11
// Read M S S S
var cigar21 = new CigarAlignment("1M3S");
var read21 = TestHelper.CreateRead("chr1", "ACGT", 8, cigar21);
Assert.Equal(false, nbhdReadFilter.IsClippedWithinNeighborhood(read21, callableNeighbor1));
// Clipped portion of read starts on first variant site -> within neighborhood
// POS 8 9 10 11
// Read M M S S
var cigar4 = new CigarAlignment("2M2S");
var read4 = TestHelper.CreateRead("chr1", "ACGT", 8, cigar4);
Assert.Equal(true, nbhdReadFilter.IsClippedWithinNeighborhood(read4, callableNeighbor1));
// Clipped portion of read starts after first variant site but before end of neighborhood -> within neighborhood
// POS 8 9 10 11
// Read M M M S
var cigar5 = new CigarAlignment("3M1S");
var read5 = TestHelper.CreateRead("chr1", "ACGT", 8, cigar5); // clipped end matches start of neighborhood
Assert.Equal(true, nbhdReadFilter.IsClippedWithinNeighborhood(read5, callableNeighbor1));
// Clipped portion of read ends before end of neighborhood -> within neighborhood
// POS 24 25 26 27
// Read S M M M
var cigar22 = new CigarAlignment("1S3M");
var read22 = TestHelper.CreateRead("chr1", "ACGT", 25, cigar22);
Assert.Equal(true, nbhdReadFilter.IsClippedWithinNeighborhood(read22, callableNeighbor1));
// Clipped portion of read ends at last variant site of neighborhood -> within neighborhood
// POS 24 25 26 27
// Read S S M M
var cigar6 = new CigarAlignment("2S2M");
var read6 = TestHelper.CreateRead("chr1", "ACGT", 26, cigar6);
Assert.Equal(true, nbhdReadFilter.IsClippedWithinNeighborhood(read6, callableNeighbor1));
// Clipped portion of read ends after neighborhood's last variant site -> NOT within neighborhood
// POS 24 25 26 27
// Read S S S M
var cigar7 = new CigarAlignment("3S1M");
var read7 = TestHelper.CreateRead("chr1", "ACGT", 27, cigar7);
Assert.Equal(false, nbhdReadFilter.IsClippedWithinNeighborhood(read7, callableNeighbor1));
// TODO (maybe test in future)
// Nima: These borders are not very necessary given we don't check exact match in first pass over clipped reads.
// Testing SoftClip position and End for neighborhoods with deletion
var neighbor2 = new VcfNeighborhood(0, "chr1", new VariantSite(10000), new VariantSite(200000))
{
VcfVariantSites = new List <VariantSite>
{
new VariantSite(10)
{
VcfReferenceAllele = "ACC", VcfAlternateAllele = "A"
},
new VariantSite(25)
{
VcfReferenceAllele = "TCC", VcfAlternateAllele = "T"
},
},
};
neighbor2.SetRangeOfInterest();
Assert.Equal(10, neighbor2.SoftClipEndBeforeNbhd);
Assert.Equal(28, neighbor2.SoftClipPosAfterNbhd);
// Testing SoftClip position and End for neighborhoods with insertion
var neighbor3 = new VcfNeighborhood(0, "chr1", new VariantSite(10000), new VariantSite(200000))
{
VcfVariantSites = new List <VariantSite>
{
new VariantSite(10)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "ACC"
},
new VariantSite(25)
{
VcfReferenceAllele = "T", VcfAlternateAllele = "TCC"
},
},
};
neighbor3.SetRangeOfInterest();
Assert.Equal(10, neighbor3.SoftClipEndBeforeNbhd);
Assert.Equal(26, neighbor3.SoftClipPosAfterNbhd);
}
public void PastNeighborhoodTest()
{
var nbhdReadFilter = new NeighborhoodReadFilter(new BamFilterParameters()
{
MinimumMapQuality = 20
});
// Scenario 1: neighborhood with 2 SNVs
var neighbor1 = new VcfNeighborhood(0, "chr1", new VariantSite(10000), new VariantSite(200000))
{
VcfVariantSites = new List <VariantSite>
{
new VariantSite(10)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "C"
},
new VariantSite(15)
{
VcfReferenceAllele = "G", VcfAlternateAllele = "A"
},
},
};
var callableNeighbor1 = new CallableNeighborhood(neighbor1, new VariantCallingParameters());
var read1 = TestHelper.CreateRead("chr1", "ACGT", 6); // ends before neighborhood starts
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read1, callableNeighbor1));
var read2 = TestHelper.CreateRead("chr1", "ACGT", 8); // read partially covers neighborhood from left
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read2, callableNeighbor1));
var read3 = TestHelper.CreateRead("chr1", "ACGT", 11); // read enclosed in neighborhood
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read3, callableNeighbor1));
var read4 = TestHelper.CreateRead("chr1", "ACGT", 14); // read partially sticks out of neighborhood from right
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read4, callableNeighbor1));
var read5 = TestHelper.CreateRead("chr1", "ACGT", 15); // read starts on last variant site
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read5, callableNeighbor1));
var read6 = TestHelper.CreateRead("chr1", "ACGT", 16); // read starts right after neighborhood
// Nima: Minimum lookahead is pos+1, so this is still not considered past neighborhood (maybe we should -1 but it doesn't really make a huge diff?)
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read6, callableNeighbor1));
var read7 = TestHelper.CreateRead("chr1", "ACGT", 17); // read starts after neighborhood lookahead
Assert.Equal(true, nbhdReadFilter.PastNeighborhood(read7, callableNeighbor1));
// Scenario 2: neighborhood with one SNV, and one insertion (should extend lookahead)
var neighbor2 = new VcfNeighborhood(0, "chr1", new VariantSite(10000), new VariantSite(200000))
{
VcfVariantSites = new List <VariantSite>
{
new VariantSite(10)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "C"
},
new VariantSite(15)
{
VcfReferenceAllele = "G", VcfAlternateAllele = "GAAA"
},
},
};
var callableNeighbor2 = new CallableNeighborhood(neighbor2, new VariantCallingParameters(), null);
var read8 = TestHelper.CreateRead("chr1", "ACGT", 15); // read starts at the last variant site
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read8, callableNeighbor2));
var read9 = TestHelper.CreateRead("chr1", "ACGT", 16); // read starts after last variant position, but before lookahead
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read9, callableNeighbor2));
var read10 = TestHelper.CreateRead("chr1", "ACGT", 17); // read starts after last variant position, but before lookahead
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read10, callableNeighbor2));
var read11 = TestHelper.CreateRead("chr1", "ACGT", 18); // read starts after last variant position, but before lookahead
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read11, callableNeighbor2));
var read12 = TestHelper.CreateRead("chr1", "ACGT", 19); // read starts after last variant position, but before lookahead
// Nima: Minimum lookahead is pos+4, so this is still not considered past neighborhood (maybe we should -1 but it doesn't really make a huge diff?)
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read12, callableNeighbor2));
var read13 = TestHelper.CreateRead("chr1", "ACGT", 20); // read starts after lookahead
Assert.Equal(true, nbhdReadFilter.PastNeighborhood(read13, callableNeighbor2));
// Scenario 3: neighborhood with one SNV, and one deletion (similar to Scenario 2)
var neighbor3 = new VcfNeighborhood(0, "chr1", new VariantSite(10000), new VariantSite(200000))
{
VcfVariantSites = new List <VariantSite>
{
new VariantSite(10)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "C"
},
new VariantSite(15)
{
VcfReferenceAllele = "GAAA", VcfAlternateAllele = "G"
},
},
};
var callableNeighbor3 = new CallableNeighborhood(neighbor3, new VariantCallingParameters(), null);
var read14 = TestHelper.CreateRead("chr1", "ACGT", 18); // read starts after last variant position, but before lookahead
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read14, callableNeighbor3));
var read15 = TestHelper.CreateRead("chr1", "ACGT", 19); // read starts after last variant position, but before lookahead
// Nima: Minimum lookahead is pos+4, so this is still not considered past neighborhood (maybe we should -1 but it doesn't really make a huge diff?)
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read15, callableNeighbor3));
var read16 = TestHelper.CreateRead("chr1", "ACGT", 20); // read starts after lookahead
Assert.Equal(true, nbhdReadFilter.PastNeighborhood(read16, callableNeighbor3));
// Scenario 4: long indel variant in the beginning of neighborhood can extend lookahead
var neighbor4 = new VcfNeighborhood(0, "chr1", new VariantSite(10000), new VariantSite(200000))
{
VcfVariantSites = new List <VariantSite>
{
new VariantSite(10)
{
VcfReferenceAllele = "A", VcfAlternateAllele = "ATTTTTTT"
},
new VariantSite(15)
{
VcfReferenceAllele = "G", VcfAlternateAllele = "A"
},
},
};
var callableNeighbor4 = new CallableNeighborhood(neighbor4, new VariantCallingParameters(), null);
var read17 = TestHelper.CreateRead("chr1", "ACGT", 16); // read starts after last variant position, but before lookahead from first variant
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read17, callableNeighbor4));
var read18 = TestHelper.CreateRead("chr1", "ACGT", 17); // read starts after last variant position, but before lookahead from first variant
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read18, callableNeighbor4));
var read19 = TestHelper.CreateRead("chr1", "ACGT", 18); // read starts after last variant position, but before lookahead from first variant
Assert.Equal(false, nbhdReadFilter.PastNeighborhood(read19, callableNeighbor4));
var read20 = TestHelper.CreateRead("chr1", "ACGT", 20); // read starts after lookahead of first variant
Assert.Equal(true, nbhdReadFilter.PastNeighborhood(read20, callableNeighbor4));
}
