private void ExecuteTest(BamAlignment read, int minBaseCallQuality, List <VariantSite> vsFromVcf, Action <Dictionary <SubsequenceType, List <VariantSite> > > setCandidatesAssertions = null,
Action <VariantSite[]> matchVariantsAssertions = null)
{
var readProcessor = new VeadFinder(new BamFilterParameters()
{
MinimumBaseCallQuality = minBaseCallQuality
});
int lastPos;
var foundVariants
= readProcessor.SetCandidateVariantsFoundInRead(minBaseCallQuality, read, out lastPos);
//if (setCandidatesAssertions != null)
//{
setCandidatesAssertions(foundVariants);
//}
var matchedVariants
= readProcessor.MatchReadVariantsWithVcfVariants(vsFromVcf, foundVariants, read.Position + 1, lastPos);
//if (matchVariantsAssertions != null)
//{
matchVariantsAssertions(matchedVariants);
//}
readProcessor.FindVariantResults(vsFromVcf, read);
}
/// <summary>
/// Note, this test is deliberately stressing the algorithm over the usecase
/// of a pathological MNV (mnvs do not really have prepended bases inside Pisces/Scylla/ect).
/// The point is to demonstrate that the method still check the whole alt allele sequence
/// is a match with the read seqeunce being queried.
/// </summary>
private static void CheckWeCanFindAnMNVInARead_pathologicalMNV()
{
var vcfSNP = new VariantSite();
vcfSNP.VcfReferencePosition = 4;
vcfSNP.VcfReferenceAllele = "ATA";
vcfSNP.VcfAlternateAllele = "ACG";
//a VS section mined from a read that indeed contains the MNV (exactly)
//what we are looking for:
// 1 2 3 4 5 6 7 8 9
// looking for -> - - - A C G - - -
// read: -> ? ? ? A C G ? ? ?
var vs1 = new VariantSite();
vs1.VcfReferencePosition = 4;
vs1.VcfReferenceAllele = "ATA";
vs1.VcfAlternateAllele = "ACG";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs1));
//a VS mined from a longer read that also contains the MNV
//what we are looking for:
// 1 2 3 4 5 6 7 8 9
// looking for -> - - - A C G - - -
// read: -> ? ? A A C G A ? ?
var vs2 = new VariantSite();
vs2.VcfReferencePosition = 3;
vs2.VcfReferenceAllele = "AATAA";
vs2.VcfAlternateAllele = "AACGA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs2));
//a VS mined from a shorter read that does NOT prove the existence of the MNV
//IN this case (to get a section this short to parse) we must have seen a whacky cigar string with only 1 match (ex, 4I1M8I)
//or we are approaching the end of the read and have one base left to check, perhaps the other bases failed filters or got softclipped.
//what we are looking for:
// 1 2 3 4 5 6 7 8 9
// looking for -> - - - A C G - - -
// read: -> ? ? ? ? C ? ? ? ?
var vs3 = new VariantSite();
vs3.VcfReferencePosition = 5;
vs3.VcfReferenceAllele = "T";
vs3.VcfAlternateAllele = "C";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs3));
//a VS section mined from a read that indeed contain a ref site
var vs4 = new VariantSite();
vs4.VcfReferencePosition = 3;
vs4.VcfReferenceAllele = "AATAA";
vs4.VcfAlternateAllele = "AATAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundReferenceVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs4));
//a VS section mined from a read that indeed contain a diff MNV site
//what we are looking for:
// 1 2 3 4 5 6 7 8 9
// looking for -> - - - A C G - - -
// read: -> ? ? G G G G G ? ?
var vs5 = new VariantSite();
vs5.VcfReferencePosition = 3;
vs5.VcfReferenceAllele = "AATAA";
vs5.VcfAlternateAllele = "GGGGG";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundDifferentVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs5));
//a VS section mined from a read that indeed contain a diff MNV site
var vs6 = new VariantSite();
vs6.VcfReferencePosition = 3;
vs6.VcfReferenceAllele = "AATAA";
vs6.VcfAlternateAllele = "AACAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundDifferentVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs6));
//We are looking for ATA -> ACG , pos 4.
//We will never find it in a sequence that starts on position 5 (as in vs7).
//We either have found pos 4 ealier, when this method was called on a previous sequence (in which case we would exit before getting here)
//~or~ all the bases at postion 4 got clipped or filtered off, which is why we are starting so late in the read.
//( -> result should be that the bases in the test sequence for pos 4 must have FailedFilters and were not available to the query method)
//what we are looking for:
// 1 2 3 4 5 6 7 8 9
// looking for -> - - - A C G - - -
// read: -> ? ? ? ? C A A ? ?
var vs7 = new VariantSite();
vs7.VcfReferencePosition = 5;
vs7.VcfReferenceAllele = "TAA";
vs7.VcfAlternateAllele = "CAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs7));
//We are looking for ATA -> ACG , pos 4.
//We will never find it in a sequence that starts on position 5 (as in vs8).
//We either have found pos 4 ealier, when this method was called on a previous sequence (in which case we would exit before getting here)
//~or~ all the bases at postion 4 got clipped or filtered off, which is why we are starting so late in the read.
//( -> result should be that the bases in the test sequence for pos 4 must have FailedFilters and were not available to the query method)
//what we are looking for:
// 1 2 3 4 5 6 7 8 9
// looking for -> - - - A C G - - -
// read: -> ? ? ? ? C G ? ? ?
var vs8 = new VariantSite();
vs8.VcfReferencePosition = 5;
vs8.VcfReferenceAllele = "TA";
vs8.VcfAlternateAllele = "CG";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs8));
}
private static void CheckWeCanFindAnMNVInARead_healthyMNV()
{
var vcfSNP = new VariantSite();
vcfSNP.VcfReferencePosition = 4;
vcfSNP.VcfReferenceAllele = "TA";
vcfSNP.VcfAlternateAllele = "CC";
//a VS mined from a read that indeed contains the MNV
var vs1 = new VariantSite();
vs1.VcfReferencePosition = 2;
vs1.VcfReferenceAllele = "AATAA";
vs1.VcfAlternateAllele = "AACCAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs1));
//a VS mined from a shorter read that also contains the MNV
var vs2 = new VariantSite();
vs2.VcfReferencePosition = 4;
vs2.VcfReferenceAllele = "TA";
vs2.VcfAlternateAllele = "CC";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs2));
//a VS mined from a read that contains a different MNV
var vs3 = new VariantSite();
vs3.VcfReferencePosition = 2;
vs3.VcfReferenceAllele = "AATAAA";
vs3.VcfAlternateAllele = "AAGCAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundDifferentVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs3));
//a VS mined from a shorter read with a different MNV
var vs4 = new VariantSite();
vs4.VcfReferencePosition = 4;
vs4.VcfReferenceAllele = "TA";
vs4.VcfAlternateAllele = "GC";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundDifferentVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs4));
//a VS mined from a read that contains a ref
var vs5 = new VariantSite();
vs5.VcfReferencePosition = 2;
vs5.VcfReferenceAllele = "AATAA";
vs5.VcfAlternateAllele = "AATAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundReferenceVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs5));
//a VS mined from a shorter read with a ref
var vs6a = new VariantSite();
vs6a.VcfReferencePosition = 4;
vs6a.VcfReferenceAllele = "TA";
vs6a.VcfAlternateAllele = "TA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundReferenceVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs6a));
//a VS mined from a shorter read with a ref
var vs6 = new VariantSite();
vs6.VcfReferencePosition = 4;
vs6.VcfReferenceAllele = "T";
vs6.VcfAlternateAllele = "T";
//Here we dont claim we found the full reference sequence we are looking for. We run off the end of the read.
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs6));
//a VS mined from a read that contains a no-call / base that failed filters. Because of the "N".
var vs7 = new VariantSite();
vs7.VcfReferencePosition = 2;
vs7.VcfReferenceAllele = "AATAA";
vs7.VcfAlternateAllele = "AANAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs7));
//a VS mined from a shorter read with a no-call / base that failed filters
var vs8 = new VariantSite();
vs8.VcfReferencePosition = 4;
vs8.VcfReferenceAllele = "TA";
vs8.VcfAlternateAllele = "NN";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs8));
}
private static void CheckWeCanFindASnpInARead()
{
var vcfSNP = new VariantSite();
vcfSNP.VcfReferencePosition = 4;
vcfSNP.VcfReferenceAllele = "T";
vcfSNP.VcfAlternateAllele = "C";
//a VS mined from a read that indeed contains the SNP
var vs1 = new VariantSite();
vs1.VcfReferencePosition = 2;
vs1.VcfReferenceAllele = "AATAA";
vs1.VcfAlternateAllele = "AACAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs1));
//a VS mined from a shorter read that also contains the SNP
var vs2 = new VariantSite();
vs2.VcfReferencePosition = 4;
vs2.VcfReferenceAllele = "T";
vs2.VcfAlternateAllele = "C";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs2));
//a VS mined from a read that contains a different SNP
var vs3 = new VariantSite();
vs3.VcfReferencePosition = 2;
vs3.VcfReferenceAllele = "AATAA";
vs3.VcfAlternateAllele = "AAGAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundDifferentVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs3));
//a VS mined from a shorter read with a different SNP
var vs4 = new VariantSite();
vs4.VcfReferencePosition = 4;
vs4.VcfReferenceAllele = "T";
vs4.VcfAlternateAllele = "G";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundDifferentVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs4));
//a VS mined from a read that contains a ref
var vs5 = new VariantSite();
vs5.VcfReferencePosition = 2;
vs5.VcfReferenceAllele = "AATAA";
vs5.VcfAlternateAllele = "AATAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundReferenceVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs5));
//a VS mined from a shorter read with a ref
var vs6 = new VariantSite();
vs6.VcfReferencePosition = 4;
vs6.VcfReferenceAllele = "T";
vs6.VcfAlternateAllele = "T";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundReferenceVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs6));
//a VS mined from a read that contains a no-call / base that failed filters
var vs7 = new VariantSite();
vs7.VcfReferencePosition = 2;
vs7.VcfReferenceAllele = "AATAA";
vs7.VcfAlternateAllele = "AANAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs7));
//a VS mined from a shorter read with a no-call / base that failed filters
var vs8 = new VariantSite();
vs8.VcfReferencePosition = 4;
vs8.VcfReferenceAllele = "T";
vs8.VcfAlternateAllele = "N";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs8));
}
private static void CheckWeCanFindARefInARead()
{
//for this case "found this varaint" or "found reference variant" are interchangeable results.
//This variant we are looking for *is* the reference.
var vcfSNP = new VariantSite();
vcfSNP.VcfReferencePosition = 4;
vcfSNP.VcfReferenceAllele = "T";
vcfSNP.VcfAlternateAllele = "T";
//a VS mined from a read that indeed contains the ref
var vs1 = new VariantSite();
vs1.VcfReferencePosition = 2;
vs1.VcfReferenceAllele = "AATAA";
vs1.VcfAlternateAllele = "AATCAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs1));
//a VS mined from a shorter read that also contains the ref
var vs2 = new VariantSite();
vs2.VcfReferencePosition = 4;
vs2.VcfReferenceAllele = "TA";
vs2.VcfAlternateAllele = "TC";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs2));
//a VS mined from a read that contains a different SNP
var vs3 = new VariantSite();
vs3.VcfReferencePosition = 2;
vs3.VcfReferenceAllele = "AATAAA";
vs3.VcfAlternateAllele = "AAGCAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundDifferentVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs3));
//a VS mined from a shorter read with a different SNP
var vs4 = new VariantSite();
vs4.VcfReferencePosition = 4;
vs4.VcfReferenceAllele = "TA";
vs4.VcfAlternateAllele = "GC";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundDifferentVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs4));
//a VS mined from a read that contains a ref
var vs5 = new VariantSite();
vs5.VcfReferencePosition = 2;
vs5.VcfReferenceAllele = "AATAA";
vs5.VcfAlternateAllele = "AATAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs5));
//a VS mined from a shorter read with a ref
var vs6a = new VariantSite();
vs6a.VcfReferencePosition = 4;
vs6a.VcfReferenceAllele = "TA";
vs6a.VcfAlternateAllele = "TA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs6a));
//a VS mined from a shorter read with a ref
var vs6 = new VariantSite();
vs6.VcfReferencePosition = 4;
vs6.VcfReferenceAllele = "T";
vs6.VcfAlternateAllele = "T";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.FoundThisVariant, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs6));
//a VS mined from a read that contains a no-call / base that failed filters. Because of the "N".
var vs7 = new VariantSite();
vs7.VcfReferencePosition = 2;
vs7.VcfReferenceAllele = "AATAA";
vs7.VcfAlternateAllele = "AANAA";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs7));
//a VS mined from a shorter read with a no-call / base that failed filters
var vs8 = new VariantSite();
vs8.VcfReferencePosition = 4;
vs8.VcfReferenceAllele = "TA";
vs8.VcfAlternateAllele = "NN";
Assert.Equal(VeadFinder.StateOfPhasingSiteInRead.HaveInsufficientData, VeadFinder.CheckVariantSequenceForMatchInVariantSiteFromRead(vcfSNP, vs8));
}
