public void TestbyStartPosition()
{
var parameters = new GeometricFilterParameters();
parameters.ExclusionStrategy = GeometricFilterParameters.ExclusionModel.Prune;
parameters.InclusionStrategy = GeometricFilterParameters.InclusionModel.ByStartPosition;
parameters.RegionOfInterestPath = Path.Combine(TestPaths.LocalTestDataDirectory, "roi.txt");
//ROI
//chr11 6415642 6415648
//chr11 6415768 6415772
var filter = new GeometricFilter(parameters);
var allelesWrongChr = CreateAllelesWith3baseDeletion(6415643, "chr4");
var allelesBeforeROI = CreateAllelesWith3baseDeletion(6415641, "chr11");
var allelesStartROI = CreateAllelesWith3baseDeletion(6415642, "chr11");
var allelesEndROI = CreateAllelesWith3baseDeletion(6415648, "chr11");
var allelesNotInROI = CreateAllelesWith3baseDeletion(6415650, "chr11");
var allelesBackInInROI = CreateAllelesWith3baseDeletion(6415771, "chr11");
var allelesAfterROI = CreateAllelesWith3baseDeletion(6415773, "chr11");
Assert.True(CheckFiltered(filter, allelesWrongChr, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesBeforeROI, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesStartROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesEndROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesNotInROI, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesBackInInROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesAfterROI, GeometricFilterParameters.ExclusionModel.Prune, false));
}
public void TestbyFilteringByExpandingTheInterval()
{
var parameters = new GeometricFilterParameters();
parameters.ExclusionStrategy = GeometricFilterParameters.ExclusionModel.Prune;
parameters.InclusionStrategy = GeometricFilterParameters.InclusionModel.Expanded;
parameters.RegionOfInterestPath = Path.Combine(TestPaths.LocalTestDataDirectory, "roi.txt");
//ROI
//chr11 6415642 6415648
//chr11 6415768 6415772
var filter = new GeometricFilter(parameters);
var allelesWrongChr = CreateSNPOnlyAlleles(6415643, "chr4");
var allelesBeforeROI = CreateSNPOnlyAlleles(6415641, "chr11");
var allelesStartROI = CreateSNPOnlyAlleles(6415642, "chr11");
var allelesEndROI = CreateSNPOnlyAlleles(6415648, "chr11");
var allelesNotInROI = CreateSNPOnlyAlleles(6415650, "chr11");
var allelesBackInInROI2 = CreateSNPOnlyAlleles(6415771, "chr11");
var allelesAfterROI2 = CreateSNPOnlyAlleles(6415773, "chr11");
Assert.True(CheckFiltered(filter, allelesWrongChr, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesBeforeROI, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesStartROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesEndROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesNotInROI, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesBackInInROI2, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesAfterROI2, GeometricFilterParameters.ExclusionModel.Prune, false));
//ROI
//chr11 6415642 6415648
//chr11 6415768 6415772
allelesWrongChr = CreateAllelesWith3baseDeletion(6415643, "chr4"); //will still be on wrong chr
var snpsBeforeROI1 = CreateSNPOnlyAlleles(6415641, "chr11"); // not in the interval yet - the deletion has not caused it to be expanded
allelesBeforeROI = CreateAllelesWith3baseDeletion(6415639, "chr11"); //3 base deletion starts on 39, and has deleted bases 40,41,42
var snpsBeforeROI2 = CreateSNPOnlyAlleles(6415641, "chr11"); //the deletion upstream should make it included in the interval when it was not before.
allelesStartROI = CreateAllelesWith3baseDeletion(6415642, "chr11");
allelesEndROI = CreateAllelesWith3baseDeletion(6415648, "chr11");
allelesNotInROI = CreateAllelesWith3baseDeletion(6415650, "chr11");
allelesBackInInROI2 = CreateAllelesWith3baseDeletion(6415771, "chr11");
allelesAfterROI2 = CreateAllelesWith3baseDeletion(6415773, "chr11");
Assert.True(CheckFiltered(filter, allelesWrongChr, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, snpsBeforeROI1, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesBeforeROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, snpsBeforeROI2, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesStartROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesEndROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesNotInROI, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesBackInInROI2, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesAfterROI2, GeometricFilterParameters.ExclusionModel.Prune, false));
//make a new filter to reset the intervals to the original positions.
filter = new GeometricFilter(parameters);
var mnvBeforeROI = CreateAllelesWith2baseMNV(6415640, "chr11"); //2 base MNV starts on 40 and extends to 41, so still out of the interval
var mnvCrossingIntoROI = CreateAllelesWith2baseMNV(6415641, "chr11"); //2 base MNV starts on 41 and extends to 42, so goes into interval + forces it to expand
var mnvInsideROI = CreateAllelesWith2baseMNV(6415648, "chr11"); //2 base MNV starts on 648
var mnvAfterROI = CreateAllelesWith2baseMNV(6415766, "chr11"); //2 base MNV starts on 766
Assert.True(CheckFiltered(filter, allelesWrongChr, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, mnvBeforeROI, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, snpsBeforeROI1, GeometricFilterParameters.ExclusionModel.Prune, false)); //SNP on pos 641
Assert.True(CheckFiltered(filter, mnvCrossingIntoROI, GeometricFilterParameters.ExclusionModel.Prune, true)); //now position 641 is IN the interval
Assert.True(CheckFiltered(filter, snpsBeforeROI2, GeometricFilterParameters.ExclusionModel.Prune, true)); //SNP on pos 641
Assert.True(CheckFiltered(filter, allelesStartROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, allelesEndROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, mnvInsideROI, GeometricFilterParameters.ExclusionModel.Prune, true));
Assert.True(CheckFiltered(filter, mnvAfterROI, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesNotInROI, GeometricFilterParameters.ExclusionModel.Prune, false));
Assert.True(CheckFiltered(filter, allelesBackInInROI2, GeometricFilterParameters.ExclusionModel.Prune, true));
}
