Exemplo n.º 1
0
        private void ExecuteGroupingTest(List <Read> reads, List <int> expectedGroupMemberships, IEnumerable <Tuple <int, string, string> > variants)
        {
            var variantSites = new List <VariantSite>();

            foreach (var variant in variants)
            {
                variantSites.Add(new VariantSite(variant.Item1)
                {
                    VcfReferenceAllele = variant.Item2, VcfAlternateAllele = variant.Item3
                });
            }

            var alignmentExtractor = new MockAlignmentExtractor(reads);

            var veadSource = new VeadGroupSource(alignmentExtractor, new BamFilterParameters()
            {
                MinimumMapQuality = 20
            }, false, "");
            var vcfNeighborhood = new VcfNeighborhood(new VariantCallingParameters(), "chr1", new VariantSite(120), new VariantSite(121), "T")
            {
                VcfVariantSites = variantSites
            };

            vcfNeighborhood.SetRangeOfInterest();

            var veadGroups = veadSource.GetVeadGroups(vcfNeighborhood).ToList();

            Assert.Equal(expectedGroupMemberships.Count, veadGroups.Count());
            for (var i = 0; i < veadGroups.Count(); i++)
            {
                Assert.Equal(expectedGroupMemberships[i], veadGroups[i].NumVeads);
            }
        }
Exemplo n.º 2
0
        public void GetVeads()
        {
            var vcfNeighborhood = new VcfNeighborhood(new VariantCallingParameters(), "chr1", new VariantSite(10000), new VariantSite(200000), "T")
            {
                VcfVariantSites = new List <VariantSite>
                {
                    new VariantSite(100)
                    {
                        VcfReferenceAllele = "A", VcfAlternateAllele = "C"
                    },
                    new VariantSite(400)
                    {
                        VcfReferenceAllele = "A", VcfAlternateAllele = "C"
                    },
                    new VariantSite(505)
                    {
                        VcfReferenceAllele = "A", VcfAlternateAllele = "C"
                    },
                    new VariantSite(703)
                    {
                        VcfReferenceAllele = "A", VcfAlternateAllele = "T"
                    },
                    new VariantSite(800)
                    {
                        VcfReferenceAllele = "A", VcfAlternateAllele = "C"
                    },
                }
            };

            var reads = new List <Read>();

            reads.Add(CreateRead("chr1", "ACGT", 10));                     // Before neighborhood
            reads.Add(CreateRead("chr1", "ACGT", 96));                     // Ends right before neighborhood's first variant site
            reads.Add(CreateRead("chr1", "ACGT", 100));                    // Match (100)
            reads.Add(CreateRead("chr1", "ACGT", 300));                    // Within neighborhood but no VariantSite
            reads.Add(CreateRead("chr1", "ACGT", 400, qualityForAll: 19)); // Within neighbhorhood but low quals
            reads.Add(CreateRead("chr1", "ACGT", 500));                    // Within neighborhood but no VariantSite (ends right before 505)
            reads.Add(CreateRead("chr1", "ACGT", 700));                    // Match (703)
            reads.Add(CreateRead("chr1", "ACGT", 800));                    // Match (800)
            reads.Add(CreateRead("chr1", "ACGT", 805));                    // Past neighborhood
            reads.Add(CreateRead("chr1", "ACGT", 900));                    // Past neighborhood
            reads.Add(CreateRead("chr2", "ACGT", 100));                    // Wrong chromosome


            vcfNeighborhood.SetRangeOfInterest();

            var alignmentExtractor = new MockAlignmentExtractor(reads);


            var veadSource = new VeadGroupSource(alignmentExtractor,
                                                 new BamFilterParameters()
            {
                MinimumMapQuality = 20
            }, false, "");

            var veadGroups = veadSource.GetVeadGroups(vcfNeighborhood);

            // Collect all reads that could relate to the neighborhood
            // - Skip anything that has quality less than MinimumMapQuality
            // - Skip anything that ends before neighborhood begins
            // - Stop collecting once we've passed the end of the neighborhood

            // We should have collected the reads at 100, 700, and 800.
            Assert.Equal(801, vcfNeighborhood.LastPositionOfInterestWithLookAhead);
            Assert.Equal(3, veadGroups.Count());
            Assert.Equal(1, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("100")));
            Assert.Equal(1, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("700")));
            Assert.Equal(1, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("800")));
            Assert.Equal(0, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("805")));
            Assert.Equal(0, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("900")));
            foreach (var veadGroup in veadGroups)
            {
                Assert.Equal(1, veadGroup.NumVeads);
            }

            vcfNeighborhood.VcfVariantSites.Add(
                new VariantSite(790)
            {
                VcfReferenceAllele = "ACAGTGAAAGACTTGTGAC", VcfAlternateAllele = "C"
            });

            vcfNeighborhood.SetRangeOfInterest();
            Assert.Equal(809, vcfNeighborhood.LastPositionOfInterestWithLookAhead);

            alignmentExtractor = new MockAlignmentExtractor(reads);


            veadSource = new VeadGroupSource(alignmentExtractor,
                                             new BamFilterParameters()
            {
                MinimumMapQuality = 20
            }, false, "");

            veadGroups = veadSource.GetVeadGroups(vcfNeighborhood);

            Assert.Equal(3, veadGroups.Count());
            Assert.Equal(1, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("100")));
            Assert.Equal(1, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("700")));
            Assert.Equal(1, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("800")));
            Assert.Equal(0, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("805")));
            Assert.Equal(0, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("900")));

            // Boundary case - read ends exactly at neighborhood's first variant site

            reads = new List <Read>();
            reads.Add(CreateRead("chr1", "ACGT", 10)); // Before neighborhood
            reads.Add(CreateRead("chr1", "ACGT", 96)); // Ends right before neighborhood's first variant site
            reads.Add(CreateRead("chr1", "ACGT", 97)); // Ends exactly at neighborhood's first variant site

            alignmentExtractor = new MockAlignmentExtractor(reads);

            veadSource = new VeadGroupSource(alignmentExtractor, new BamFilterParameters()
            {
                MinimumMapQuality = 20
            }, false, "");

            veadGroups = veadSource.GetVeadGroups(vcfNeighborhood);

            // The veadgroup for 97 should be the only one
            Assert.Equal(1, veadGroups.Count());
            Assert.Equal(1, veadGroups.Count(v => v.RepresentativeVead.Name.EndsWith("97")));
            foreach (var veadGroup in veadGroups)
            {
                Assert.Equal(1, veadGroup.NumVeads);
            }
        }