public void ColumnsSetters()
{
// Arrange
var rg = new RegionGenerator
{
ChrColumn = 2,
PositionColumn = 2,
IDColumn = 9,
RefbColumn = 0,
AltbColumn = 2,
QualityColumn = 2,
FilterColumn = 0,
InfoColumn = 6,
StrandColumn = 12
};
rg.InfoColumn = 12;
using (var file = new TempFileCreator(rg))
{
// Act
var parsedVCF = ParseVCF(file.TempFilePath, rg);
var parsedPeak = parsedVCF.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedPeak.CompareTo(rg.Variant) == 0);
}
}
public void TestColumnsShuffle(
byte chrColumn, byte positionColumn, byte idColumn, byte refBPColumn, byte altBPColumn,
byte qualityColumn, byte filterColumn, byte infoColumn, sbyte strandColumn)
{
// Arrange
var rg = new RegionGenerator()
{
ChrColumn = chrColumn,
PositionColumn = positionColumn,
IDColumn = idColumn,
RefbColumn = refBPColumn,
AltbColumn = altBPColumn,
QualityColumn = qualityColumn,
FilterColumn = filterColumn,
InfoColumn = infoColumn,
StrandColumn = strandColumn
};
using (var file = new TempFileCreator(rg))
{
// Act
var parsedVCF = ParseVCF(file.TempFilePath, rg);
var parsedVariant = parsedVCF.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedVariant.CompareTo(rg.Variant) == 0);
}
}
public void AssignHashKey()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new VcfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0].GetHashCode() != 0);
}
}
public void TestDefaultVCFColumnOrder()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new VcfParser();
var parsedVariant = parser.Parse(file.TempFilePath).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedVariant.CompareTo(rg.Variant) == 0);
}
}
public void OneBaseLenghtInterval()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new VcfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0].Right == rg.Position + 1);
}
}
public void FullySetArguments()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new VcfParser(rg.Columns);
var parsedVariant = parser.Parse(file.TempFilePath).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0];
// Assert
Assert.True(parsedVariant.CompareTo(rg.Variant) == 0);
}
}
public void MultiVariantFile()
{
// Arrange
var rg = new RegionGenerator {
StrandColumn = 12
};
using (var file = new TempFileCreator(rg, variantsCount: 10, headerLineCount: 2))
{
// Act
var parser = new VcfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.Count == 10);
}
}
public void FailToReadID()
{
// Arrange
var rg = new RegionGenerator()
{
IDColumn = 20
};
string line = "chr1\t10\tAAC\tCCA\t123.456\tFilter\tInfo\t*";
using (var file = new TempFileCreator(line))
{
// Act
var parsedVCF = ParseVCF(file.TempFilePath, rg);
// Assert
Assert.False(parsedVCF.Chromosomes.ContainsKey("chr1"));
}
}
public TempFileCreator(RegionGenerator columns, int headerLineCount = 0, int variantsCount = 1)
{
TempFilePath = Path.GetTempPath() + Guid.NewGuid().ToString() + ".vcf";
FileStream stream = File.Create(TempFilePath);
using (StreamWriter writer = new StreamWriter(stream))
{
while (headerLineCount-- > 0)
{
writer.WriteLine(columns.GetSampleHeader());
}
while (variantsCount-- > 0)
{
writer.WriteLine(columns.GetSampleLine());
if (variantsCount > 0)
{
columns.Position += 10;
}
}
}
}
private Vcf <Variant> ParseVCF(string filePath, RegionGenerator rg)
{
var parser = new VcfParser(rg.Columns);
return(parser.Parse(filePath));
}