public void IndelWithNoLeadingBase()
{
var tsvReader = new StreamReader(new MemoryStream());
var vcfReader = new StreamReader(new MemoryStream());
var cosmicReader = new MergedCosmicReader(vcfReader, tsvReader, _refChromDict);
const string vcfLine1 = "3 10188320 COSM14426 GGTACTGAC A . . GENE=VHL;STRAND=+;CDS=c.463G>A;AA=p.?;CNT=2";
const string vcfLine2 = "3 10188320 COSM18152 G A . . GENE=VHL;STRAND=+;CDS=c.463G>A;AA=p.V155M;CNT=7";
var items = cosmicReader.ExtractCosmicItems(vcfLine1);
Assert.Equal("GGTACTGAC", items[0].ReferenceAllele);
Assert.Equal("A", items[0].AlternateAllele);
Assert.Equal(10188320, items[0].Start);
var items2 = cosmicReader.ExtractCosmicItems(vcfLine2);
Assert.Equal("G", items2[0].ReferenceAllele);
Assert.Equal("A", items2[0].AlternateAllele);
Assert.Equal(10188320, items2[0].Start);
}
public void IndelWithNoLeadingBase()
{
var seqProvider = ParserTestUtils.GetSequenceProvider(10188320, "GGTACTGAC", 'A', ChromosomeUtilities.RefNameToChromosome);
//the files provided are just for the sake of construction. The main aim is to test the VCF line parsing capabilities
var cosmicReader = new MergedCosmicReader(Resources.TopPath("cosm5428243.vcf"), Resources.TopPath("cosm5428243.tsv"), seqProvider);
const string vcfLine1 = "3 10188320 COSM14426 GGTACTGAC A . . GENE=VHL;STRAND=+;CDS=c.463G>A;AA=p.?;CNT=2";
const string vcfLine2 = "3 10188320 COSM18152 G A . . GENE=VHL;STRAND=+;CDS=c.463G>A;AA=p.V155M;CNT=7";
var items = cosmicReader.ExtractCosmicItems(vcfLine1);
Assert.Equal("GGTACTGAC", items[0].RefAllele);
Assert.Equal("A", items[0].AltAllele);
Assert.Equal(10188320, items[0].Position);
var items2 = cosmicReader.ExtractCosmicItems(vcfLine2);
Assert.Equal("G", items2[0].RefAllele);
Assert.Equal("A", items2[0].AltAllele);
Assert.Equal(10188320, items2[0].Position);
}
public void IndelWithNoLeadingBase()
{
var cosmicReader = new MergedCosmicReader();
const string vcfLine1 = "3 10188320 COSM14426 GGTACTGAC A . . GENE=VHL;STRAND=+;CDS=c.463G>A;AA=p.?;CNT=2";
const string vcfLine2 = "3 10188320 COSM18152 G A . . GENE=VHL;STRAND=+;CDS=c.463G>A;AA=p.V155M;CNT=7";
var sa = new SupplementaryAnnotationPosition(10188320);
var saCreator = new SupplementaryPositionCreator(sa);
foreach (var cosmicItem in cosmicReader.ExtractCosmicItems(vcfLine1))
{
cosmicItem.SetSupplementaryAnnotations(saCreator);
}
Assert.Equal("9A", sa.CosmicItems[0].SaAltAllele);
foreach (var cosmicItem in cosmicReader.ExtractCosmicItems(vcfLine2))
{
cosmicItem.SetSupplementaryAnnotations(saCreator);
}
Assert.Equal("A", sa.CosmicItems[1].SaAltAllele);
}