public void FastForward_EnsemblNamingStyle_ChangeReaderStateCorrectly()
{
var annotationRange = new GenomicRange(new GenomicPosition(ChromosomeUtilities.Chr1, 100), new GenomicPosition(ChromosomeUtilities.Chr1, 200));
var vcfFilter = new VcfFilter(annotationRange);
const string firstLineInRange = "1\t100\t.\tC\tT\t165.00\tPASS\tSNVSB=-12.5;SNVHPOL=2\tGT:GQ:GQX:DP:DPF:AD\t0/1:119:35:25:0:8,17";
using (var ms = new MemoryStream())
{
using (var writer = new StreamWriter(ms, Encoding.UTF8, 1024, true))
{
writer.WriteLine("#Header line 1");
writer.WriteLine("#Header line 2");
writer.WriteLine("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tMother");
writer.WriteLine("2\t150\t.\tG\tA\t5.00\tLowGQXHetSNP\tSNVSB=0.0;SNVHPOL=2\tGT:GQ:GQX:DP:DPF:AD\t0/1:3:1:1:0:0,1");
writer.WriteLine("1\t90\t.\tT\tC\t1.00\tLowGQXHetSNP\tSNVSB=0.0;SNVHPOL=2\tGT:GQ:GQX:DP:DPF:AD\t0/1:23:9:3:0:2,1");
writer.WriteLine("1\t95\t.\tA\tT\t2.00\tLowGQXHetSNP\tSNVSB=0.0;SNVHPOL=2\tGT:GQ:GQX:DP:DPF:AD\t0/1:23:9:3:0:2,1");
writer.WriteLine(firstLineInRange);
writer.WriteLine("1\t102\t.\tC\tA\t3.00\tLowGQXHetSNP\tSNVSB=0.0;SNVHPOL=5\tGT:GQ:GQX:DP:DPF:AD\t0/1:29:2:2:0:1,1");
}
ms.Position = 0;
using (var reader = new StreamReader(ms))
{
vcfFilter.FastForward(reader);
Assert.Equal(firstLineInRange, vcfFilter.BufferedLine);
}
}
}
public void PassedTheEnd_AsExpected()
{
var annotationRange = new GenomicRange(new GenomicPosition(ChromosomeUtilities.Chr1, 100), new GenomicPosition(ChromosomeUtilities.Chr1, 200));
var vcfFilter = new VcfFilter(annotationRange);
Assert.False(vcfFilter.PassedTheEnd(ChromosomeUtilities.Chr1, 150));
Assert.False(vcfFilter.PassedTheEnd(ChromosomeUtilities.Chr1, 200));
Assert.True(vcfFilter.PassedTheEnd(ChromosomeUtilities.Chr1, 201));
Assert.True(vcfFilter.PassedTheEnd(ChromosomeUtilities.Chr2, 150));
}
public void GetNextLine_NoBufferedLine_ReadNextLine()
{
var vcfFilter = new VcfFilter(null);
using (var ms = new MemoryStream(Encoding.UTF8.GetBytes("first line\nsecond line\n")))
using (var reader = new StreamReader(ms))
{
string nextLine = vcfFilter.GetNextLine(reader);
Assert.Equal("first line", nextLine);
}
}
public void PassedTheEnd_AsExpected()
{
var chromosome = new Chromosome("chr1", "1", 0);
var annotationRange = new GenomicRange(new GenomicPosition(chromosome, 100), new GenomicPosition(chromosome, 200));
var vcfFilter = new VcfFilter(annotationRange);
Assert.False(vcfFilter.PassedTheEnd(new Chromosome("chr1", "1", 0), 150));
Assert.False(vcfFilter.PassedTheEnd(new Chromosome("chr1", "1", 0), 200));
Assert.True(vcfFilter.PassedTheEnd(new Chromosome("chr1", "1", 0), 201));
Assert.True(vcfFilter.PassedTheEnd(new Chromosome("chr2", "2", 1), 150));
}
public void GetNextLine_ReturnBufferedLine()
{
const string bufferedLine = "I am buffered";
var vcfFilter = new VcfFilter(null)
{
BufferedLine = bufferedLine
};
string nextLine = vcfFilter.GetNextLine(null);
Assert.Equal(bufferedLine, nextLine);
}
