コード例 #1
0
        public void VarCallsBecomeRefsAndNulls()
        {
            var originalVcfVariant  = TestHelper.CreateDummyAllele("chr1", 123, "A", "T", 1000, 156);
            var originalVcfVariant2 = TestHelper.CreateDummyAllele("chr1", 124, "A", "T", 1000, 156);
            var vs1 = new VariantSite(originalVcfVariant);
            var vs2 = new VariantSite(originalVcfVariant2);

            var vcParams = new VariantCallingParameters();

            vcParams.Validate();
            var caller = new VariantCaller(vcParams, new BamFilterParameters());

            //since there is an alt at position 124 ( a call of 156 alt / 1000 total, that means 844 original ref calls.
            //Of which we said, 100 will get sucked up. So that leaves 744 / 1000 calls for a reference.
            //So, we can still make a confident ref call.

            var nbhd = new VcfNeighborhood(vcParams, 0, "chr1", vs1, vs2, "");

            nbhd.SetRangeOfInterest();
            nbhd.AddAcceptedPhasedVariant(
                new CalledAllele(AlleleCategory.Snv)
            {
                Chromosome        = "chr1",
                ReferencePosition = 123,
                ReferenceAllele   = "A",
                AlternateAllele   = "T",
                VariantQscore     = 100,
                TotalCoverage     = 1000,
                AlleleSupport     = 500
            });
            nbhd.UsedRefCountsLookup = new Dictionary <int, SuckedUpRefRecord>()
            {
            };

            caller.CallMNVs(nbhd);
            caller.CallRefs(nbhd);

            var acceptedMNVs = nbhd.CalledVariants;
            var acceptedRefs = nbhd.CalledRefs;

            Assert.Equal(1, acceptedMNVs.Count);
            Assert.Equal(1, acceptedMNVs[123].Count);

            Assert.Equal(2, acceptedRefs.Count);


            var vcfVariant2asRef = new VcfVariant()
            {
                ReferenceName     = "chr1",
                ReferencePosition = 124,
                ReferenceAllele   = "A",
                VariantAlleles    = new[] { "." },
                Genotypes         = new List <Dictionary <string, string> >()
                {
                    new Dictionary <string, string>()
                    {
                        { "GT", "0/." }, { "DP", "1000" }, { "AD", "844" }
                    }
                },
            };

            VcfMergerTests.CheckVariantsMatch(originalVcfVariant, acceptedMNVs[123][0]);
            VcfMergerTests.CheckVariantsMatch(vcfVariant2asRef, acceptedRefs[124]);

            // If one has been sucked up and there are refs remaining, we should output it as a ref.
            var suckedUpRefRecord100 = new SuckedUpRefRecord()
            {
                Counts = 100, AlleleThatClaimedIt = new CalledAllele()
            };

            nbhd.UsedRefCountsLookup = new Dictionary <int, SuckedUpRefRecord>()
            {
                { 124, suckedUpRefRecord100 }
            };


            caller.CallMNVs(nbhd);
            caller.CallRefs(nbhd);

            acceptedMNVs = nbhd.CalledVariants;
            acceptedRefs = nbhd.CalledRefs;

            Assert.Equal(1, acceptedMNVs.Count);
            Assert.Equal(1, acceptedMNVs[123].Count);

            Assert.Equal(2, acceptedRefs.Count);

            vcfVariant2asRef = new VcfVariant()
            {
                ReferenceName     = "chr1",
                ReferencePosition = 124,
                ReferenceAllele   = "A",
                VariantAlleles    = new[] { "." },
                Genotypes         = new List <Dictionary <string, string> >()
                {
                    new Dictionary <string, string>()
                    {
                        { "GT", "0/." }, { "DP", "1000" }, { "AD", "744" }
                    }
                },
            };

            VcfMergerTests.CheckVariantsMatch(originalVcfVariant, acceptedMNVs[123][0]);
            VcfMergerTests.CheckVariantsMatch(vcfVariant2asRef, acceptedRefs[124]);


            // If one has been sucked up all the way
            // we should output it as a null.
            var suckedUpRefRecord1000 = new SuckedUpRefRecord()
            {
                Counts = 1000, AlleleThatClaimedIt = new CalledAllele()
            };

            nbhd.UsedRefCountsLookup = new Dictionary <int, SuckedUpRefRecord>()
            {
                { 124, suckedUpRefRecord1000 }
            };

            caller.CallMNVs(nbhd);
            caller.CallRefs(nbhd);

            acceptedMNVs = nbhd.CalledVariants;
            acceptedRefs = nbhd.CalledRefs;

            Assert.Equal(1, acceptedMNVs.Count);
            Assert.Equal(1, acceptedMNVs[123].Count);

            Assert.Equal(2, acceptedRefs.Count);

            var vcfVariant2asNull = new VcfVariant()
            {
                ReferenceName     = "chr1",
                ReferencePosition = 124,
                ReferenceAllele   = "A",
                VariantAlleles    = new[] { "." },
                Genotypes         = new List <Dictionary <string, string> >()
                {
                    new Dictionary <string, string>()
                    {
                        { "GT", "./." }, { "DP", "1000" }, { "AD", "0" }
                    }
                },
            };

            VcfMergerTests.CheckVariantsMatch(originalVcfVariant, acceptedMNVs[123][0]);
            VcfMergerTests.CheckVariantsMatch(vcfVariant2asNull, acceptedRefs[124]);
        }
コード例 #2
0
        public void CallAVariantInANewLocation()
        {
            //set up the original variants
            var originalVcfVariant1 = TestHelper.CreateDummyAllele("chr1", 123, "A", "T", 1000, 156);
            var originalVcfVariant2 = TestHelper.CreateDummyAllele("chr1", 124, "A", "T", 1000, 156);
            var originalVcfVariant3 = TestHelper.CreateDummyAllele("chr1", 234, "A", "T", 1000, 156);
            var originalVcfVariant4 = TestHelper.CreateDummyAllele("chr1", 234, "A", "T", 1000, 156);

            var vs1 = new VariantSite(originalVcfVariant1);
            var vs2 = new VariantSite(originalVcfVariant2);
            var vs3 = new VariantSite(originalVcfVariant3);
            var vs4 = new VariantSite(originalVcfVariant4);

            var vcParams = new VariantCallingParameters();

            vcParams.Validate();
            var caller = new VariantCaller(vcParams, new BamFilterParameters());
            var nbhd   = new VcfNeighborhood(vcParams, 0, "chr1", vs1, vs2, "");

            nbhd.AddVariantSite(vs3, "RRRRR"); //note, we do not add vs4, that is not going to get used for phasing. Sps it is a variant that failed filters.
            nbhd.SetRangeOfInterest();

            //now stage one candidate MNV:
            var newMNV = new CalledAllele(AlleleCategory.Snv)
            {
                Chromosome        = "chr1",
                ReferencePosition = 129,
                ReferenceAllele   = "A",
                AlternateAllele   = "TT",
                VariantQscore     = 100,
                TotalCoverage     = 1000,
                AlleleSupport     = 500
            };


            nbhd.AddAcceptedPhasedVariant(newMNV);
            var suckedUpRefRecord1000 = new SuckedUpRefRecord()
            {
                Counts = 1000, AlleleThatClaimedIt = new CalledAllele()
            };

            nbhd.UsedRefCountsLookup = new Dictionary <int, SuckedUpRefRecord>()
            {
                { 124, suckedUpRefRecord1000 }
            };

            caller.CallMNVs(nbhd);
            caller.CallRefs(nbhd);

            var acceptedMNVs = nbhd.CalledVariants;
            var acceptedRefs = nbhd.CalledRefs;


            var vcfVariant0asRef = new VcfVariant()
            {
                ReferenceName     = "chr1",
                ReferencePosition = 123,
                ReferenceAllele   = "A",
                VariantAlleles    = new[] { "." },
                Genotypes         = new List <Dictionary <string, string> >()
                {
                    new Dictionary <string, string>()
                    {
                        { "GT", "0/." }
                    }
                },
            };

            var vcfVariant3asRef = new VcfVariant()
            {
                ReferenceName     = "chr1",
                ReferencePosition = 234,
                ReferenceAllele   = "A",
                VariantAlleles    = new[] { "." },
                Genotypes         = new List <Dictionary <string, string> >()
                {
                    new Dictionary <string, string>()
                    {
                        { "GT", "0/." }
                    }
                },
            };

            var vcfVariant2asNull = new VcfVariant()
            {
                ReferenceName     = "chr1",
                ReferencePosition = 124,
                ReferenceAllele   = "A",
                VariantAlleles    = new[] { "." },
                Genotypes         = new List <Dictionary <string, string> >()
                {
                    new Dictionary <string, string>()
                    {
                        { "GT", "./." }
                    }
                },
            };

            Assert.Equal(1, acceptedMNVs.Count);
            Assert.Equal(1, acceptedMNVs[129].Count);

            Assert.Equal(3, acceptedRefs.Count);

            VcfMergerTests.CheckVariantsMatch(vcfVariant0asRef, acceptedRefs[123]);
            VcfMergerTests.CheckVariantsMatch(vcfVariant2asNull, acceptedRefs[124]);
            VcfMergerTests.CheckVariantsMatch(newMNV, acceptedMNVs[129][0]);
            VcfMergerTests.CheckVariantsMatch(vcfVariant3asRef, acceptedRefs[234]);
        }