public void ParseHeaderLines_InconsistentFields()
{
const string invalidHeaderLines = "#title=IcslAlleleFrequencies\n" +
"#assembly=GRCh38\n" +
"#CHROM\tPOS\tREF\tALT\tEND\tallAc\tallAn\tallAf\tfailedFilter\tpathogenicity\n" +
"#categories\t.\t.\t.\t.\tAlleleCount\tAlleleNumber\tAlleleFrequency\t.\tPrediction\t.\tMore\n" +
"#descriptions\t.\t.\t.\t.\tALL\tALL\tALL\n" +
"#type\t.\t.\t.\t.\tnumber\tnumber\tnumber\tbool\tstring\tstring";
using (var parser = new VariantAnnotationsParser(GetReadStream(invalidHeaderLines), null))
{
Assert.Throws <UserErrorException>(() => parser.ParseHeaderLines());
}
}
public void ParseHeaderLines_AsExpected()
{
const string headerLines = "#title=IcslAlleleFrequencies \n" +
"#assembly=GRCh38\t\n" +
"#matchVariantsBy=allele\n" +
"#CHROM\tPOS\tREF\tALT\tEND\tallAc\tallAn\tallAf\tfailedFilter\tpathogenicity\tdeNovoQual\tnotes\n" +
"#categories\t.\t.\t.\t.\tAlleleCount\tAlleleNumber\tAlleleFrequency\t.\tPrediction\tScore\t.\n" +
"#descriptions\t.\t.\t.\t.\tALL\tALL\tALL\t.\t.\t.\t.\n" +
"#type\t.\t.\t.\t.\tnumber\tnumber\tnumber\tbool\tstring\tnumber\tstring";
using (var custParser = new VariantAnnotationsParser(GetReadStream(headerLines), null))
{
custParser.ParseHeaderLines();
var expectedJsonKeys = new[]
{ "refAllele", "altAllele", "allAc", "allAn", "allAf", "failedFilter", "pathogenicity", "deNovoQual", "notes" };
var expectedIntervalJsonKeys = new[]
{ "start", "end", "allAc", "allAn", "allAf", "failedFilter", "pathogenicity", "deNovoQual", "notes" };
var expectedCategories = new[]
{
CustomAnnotationCategories.AlleleCount, CustomAnnotationCategories.AlleleNumber,
CustomAnnotationCategories.AlleleFrequency, CustomAnnotationCategories.Unknown,
CustomAnnotationCategories.Prediction, CustomAnnotationCategories.Score,
CustomAnnotationCategories.Unknown
};
var expectedDescriptions = new[] { "ALL", "ALL", "ALL", null, null, null, null };
var expectedTypes = new[]
{
SaJsonValueType.Number,
SaJsonValueType.Number,
SaJsonValueType.Number,
SaJsonValueType.Bool,
SaJsonValueType.String,
SaJsonValueType.Number,
SaJsonValueType.String
};
Assert.Equal("IcslAlleleFrequencies", custParser.JsonTag);
Assert.Equal(GenomeAssembly.GRCh38, custParser.Assembly);
Assert.Equal(expectedJsonKeys, custParser.JsonKeys);
Assert.Equal(expectedIntervalJsonKeys, custParser.IntervalJsonKeys);
Assert.Equal(expectedCategories, custParser.Categories);
Assert.Equal(expectedDescriptions, custParser.Descriptions);
Assert.Equal(expectedTypes, custParser.ValueTypes);
}
}
public void ParseHeaderLines_matchBy_sv()
{
const string headerLines = "#title=IcslAlleleFrequencies\n" +
"#assembly=GRCh38\n" +
"#matchVariantsBy=sv\n" +
"#CHROM\tPOS\tREF\tALT\tEND\tallAc\tallAn\tallAf\tfailedFilter\tpathogenicity\tnotes\n" +
"#categories\t.\t.\t.\t.\tAlleleCount\tAlleleNumber\tAlleleFrequency\t.\tPrediction\t.\n" +
"#descriptions\t.\t.\t.\t.\tALL\tALL\tALL\t.\t.\t.\n" +
"#type\t.\t.\t.\t.\tnumber\tnumber\tnumber\tbool\tstring\tstring";
using (var custParser = new VariantAnnotationsParser(GetReadStream(headerLines), null))
{
custParser.ParseHeaderLines();
Assert.Equal(ReportFor.StructuralVariants, custParser.ReportFor);
}
}
