public void InsertionAtRegFeatureStart()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENSR00001625040_chr11_Ensembl84_reg"),
"11\t121973583\t.\tC\tCA\t.\tRepeat;QSI_ref SOMATIC;QSI=29;TQSI=1;NT=hom;QSI_NT=29;TQSI_NT=1;SGT=hom->het;RU=A;RC=9;IC=10;IHP=10 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50\t52:52:0,0:49,49:3,3:54.96:0.00:0.00\t131:131:34,34:77,77:19,19:130.89:1.24:0.00");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(1, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First();
Assert.NotNull(altAllele);
AssertUtilities.CheckRegulatoryCount(0, altAllele);
}
public void VepMissingRegulatoryFeature()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENSR00000554042_chr1_Ensembl84_reg"),
"1 225615945 . T C . PASS SOMATIC;QSS=78;TQSS=1;NT=ref;QSS_NT=78;TQSS_NT=1;SGT=TT->CT;DP=159;MQ=60.00;MQ0=0;ALTPOS=44;ALTMAP=26;ReadPosRankSum=-0.92;SNVSB=0.00;PNOISE=0.00;PNOISE2=0.00;VQSR=9.59 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 48:0:0:0:0,0:1,1:1,1:46,46 111:6:0:0:0,0:29,33:1,2:75,76");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(1, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First();
Assert.NotNull(altAllele);
AssertUtilities.CheckRegulatoryCount(1, altAllele);
var regulatoryRegion = altAllele.RegulatoryRegions.FirstOrDefault();
Assert.NotNull(regulatoryRegion);
Assert.Equal("ENSR00000554042", regulatoryRegion.ID);
}
