public void GetAllPositions()
{
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', _chromDict);
var positions = PreLoadUtilities.GetPositions(GetVcfStream(), null, seqProvider);
Assert.Equal(2, positions.Count);
Assert.Equal(4, positions[Chrom1].Count);
Assert.Equal(4, positions[Chrom2].Count);
}
public void GetPositions_inRange()
{
var chromosome = new Chromosome("chr1", "1", 0);
var annotationRange = new GenomicRange(new GenomicPosition(chromosome, 10019), new GenomicPosition(chromosome, 10290));
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', _chromDict);
var positions = PreLoadUtilities.GetPositions(GetVcfStream(), annotationRange, seqProvider);
Assert.Single(positions);
Assert.Equal(3, positions[Chrom1].Count);
}
public void GetPositions_inRange()
{
var annotationRange = new GenomicRange(new GenomicPosition(ChromosomeUtilities.Chr1, 10019), new GenomicPosition(ChromosomeUtilities.Chr1, 10290));
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', ChromosomeUtilities.RefNameToChromosome);
(var positions, _) = PreLoadUtilities.GetPositions(GetVcfStream(), annotationRange, seqProvider, null);
Assert.Single(positions);
Assert.Equal(3, positions[ChromosomeUtilities.Chr1].Count);
}
public void GetAllPositions()
{
//we only need the sequence provider for variant rotation.
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', ChromosomeUtilities.RefNameToChromosome);
(var positions, _) = PreLoadUtilities.GetPositions(GetVcfStream(), null, seqProvider, null);
Assert.Equal(2, positions.Count);
Assert.Equal(4, positions[ChromosomeUtilities.Chr1].Count);
Assert.Equal(4, positions[ChromosomeUtilities.Chr2].Count);
}
public void GetAllPositions_skip_refs()
{
//we only need the sequence provider for variant rotation.
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', ChromosomeUtilities.RefNameToChromosome);
var refMinorProvider = ParserTestUtils.GetRefMinorProvider(
new List <(IChromosome chrom, int position, string globalMinor)>
{
(ChromosomeUtilities.Chr1, 10275, "A")
}
);
(var positions, _) = PreLoadUtilities.GetPositions(GetRefMinorVcfStream(), null, seqProvider, refMinorProvider);
Assert.Equal(2, positions.Count);
Assert.Equal(5, positions[ChromosomeUtilities.Chr1].Count);
Assert.Equal(4, positions[ChromosomeUtilities.Chr2].Count);
}