public void GetNextVariantTests()
{
var resultVariant = new CalledAllele();
var resultVariants = new List <CalledAllele> {
resultVariant
};
string resultString = string.Empty;
var vr = new AlleleReader(VcfTestFile_1);
vr.GetNextVariants(out resultVariants, out resultString);
Assert.Equal(resultString.TrimEnd('\r'), @"chr1 10 . A . 25 PASS DP=500 GT:GQ:AD:VF:NL:SB:NC 1/1:25:0,0:0.0000:23:0.0000:0.0010");
Assert.Equal(resultVariants[0].Chromosome, "chr1");
Assert.Equal(resultVariants[0].ReferenceAllele, "A");
Assert.Equal(resultVariants[0].AlternateAllele, ".");
//Note, we have seen this assert below fail for specific user configurations
//When it fails the error mesg is as below:
//Assert.Equal() Failure
//Expected: 1428
//Actual: 1452
//If this happens to you, check your git attributes config file.
//You might be handling vcf text file line endings differently so the white space counts differently in this test.
// In that case, the fail is purely cosmetic.
//
//try: Auto detect text files and perform LF normalization
//# http://davidlaing.com/2012/09/19/customise-your-gitattributes-to-become-a-git-ninja/
//*text = auto
//*.cs diff = csharp
//*.bam binary
//*.vcf text
//.fa text eol = crlf
if (vr.Position() == 1428)
{
Console.WriteLine("This isn't critical, but you might want to change your line endings convention. ");
Console.WriteLine("This project was developed with \\CR\\LF , not \\LF convention.");
}
else
{
Assert.Equal(1452, vr.Position());
}
var resultStringArray = new string[] { };
resultVariant = new CalledAllele();
resultVariants = new List <CalledAllele> {
resultVariant
};
vr.GetNextVariants(out resultVariants, out resultString);
Assert.Equal(resultString.TrimEnd('\r'), @"chr1 20 . A T 25 PASS DP=500 GT:GQ:AD:VF:NL:SB:NC 1/1:25:0,0:0.0000:23:0.0000:0.0010");
for (var i = 0; i < resultStringArray.Length; i++)
{
resultStringArray[i] = resultStringArray[i].TrimEnd('\r');
}
Assert.Equal(resultVariants[0].Chromosome, "chr1");
resultVariant = new CalledAllele();
resultVariants = new List <CalledAllele> {
resultVariant
};
vr.GetNextVariants(out resultVariants);
Assert.Equal(resultVariants[0].Chromosome, "chr1");
Assert.Equal(resultVariants[0].ReferenceAllele, "A");
Assert.Equal(resultVariants[0].AlternateAllele, "AT");
}