public void IntergenicVariant()
{
var sa = new SupplementaryAnnotationPosition(47960)
{
IsRefMinorAllele = true,
GlobalMajorAllele = "A",
GlobalMajorAlleleFrequency = "0.9239"
};
var saReader = new MockSupplementaryAnnotationReader(sa);
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000518655_chr1_Ensembl84"), saReader,
"chr1 47960 . T . 1242.00 PASS SNVSB=-87.0;SNVHPOL=3");
Assert.NotNull(annotatedVariant);
Assert.Contains("\"isReferenceMinorAllele\":true", annotatedVariant.ToString());
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.FirstOrDefault();
Assert.NotNull(altAllele);
// intergenic variant are not exposed in the JSON file
AssertUtilities.CheckEnsemblTranscriptCount(0, altAllele);
AssertUtilities.CheckRefSeqTranscriptCount(0, altAllele);
}
public void MultiAlleleProteinAlteringVariant()
{
// GGGACTGGA|protein_altering_variant|MODIFIER||91544|Transcript|NM_183008.2|protein_coding|16/16||NM_183008.2:c.1501_1533delinsTCCAGTCCC|NP_892120.2:p.Pro501_Pro509delinsSer|1774-1806|1501-1533|501-511|PSPGPGPGPSP/SSP|CCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/TCCAGTCCC|||-1|||YES||NP_892120.2|rseq_mrna_match&rseq_ens_match_cds||||||||
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("NM_183008_chr1_RefSeq84"),
"chr1\t26608819\t.\tAGGGACTGGGGCCGGGACCGGGACCGGGACTGGG\tAGGGACTGGG,AGGGACTGGA\t60\tPASS\tCIGAR=1M24D9M,9M25D1I;RU=.,.;REFREP=3,.;IDREP=2,.;GMAF=A|0.3934;cosmic=COSM3749046;CSQT=1|CEP85|NM_022778.3|downstream_gene_variant,2|CEP85|NM_022778.3|downstream_gene_variant,1|SH3BGRL3|NM_031286.3|downstream_gene_variant,2|SH3BGRL3|NM_031286.3|downstream_gene_variant,1|UBXN11|NM_183008.2|inframe_deletion,2|UBXN11|NM_183008.2|\tGT:GQ:GQX:DPI:AD\t1/2:143:119:23:0,3,3");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(2, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.ElementAt(1);
Assert.NotNull(altAllele);
AssertUtilities.CheckRefSeqTranscriptCount(1, altAllele);
var transcript = altAllele.RefSeqTranscripts.FirstOrDefault();
Assert.NotNull(transcript);
// ReSharper disable once PossibleNullReferenceException
var observedConsequence = string.Join("&", transcript.Consequence);
const string expectedConsequence = "protein_altering_variant";
Assert.Equal(expectedConsequence, observedConsequence);
}
public void NoConsequences()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("chr1_115256529_G_TAA_RefSeq84_pos"),
"chr1 115256529 . T . . PASS . GT:GQX:DP:DPF 0/0:99:34:2");
Assert.NotNull(annotatedVariant);
Assert.DoesNotContain("\"isReferenceMinorAllele\":true", annotatedVariant.ToString());
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.FirstOrDefault();
Assert.NotNull(altAllele);
// intergenic variant are not exposed in the JSON file
AssertUtilities.CheckEnsemblTranscriptCount(0, altAllele);
AssertUtilities.CheckRefSeqTranscriptCount(0, altAllele);
}
public void CdnaPositionShouldNotBeReported()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("NM_005101_chr1_RefSeq84"), null,
"1 948846 . T TA . . .");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(1, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First();
Assert.NotNull(altAllele);
AssertUtilities.CheckRefSeqTranscriptCount(1, altAllele);
Assert.Null(altAllele.RefSeqTranscripts.First().ComplementaryDnaPosition);
}
public void SpliceRegionAndNonCodingExonTranscript()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("NR_026752_chr1_RefSeq84"),
"chr1 16952993 rs942268 C G . . CSQ=G|84809|NR_026752.1|Transcript|splice_region_variant&non_coding_transcript_exon_variant&non_coding_transcript_variant|347||||||4/7|||||||||||NR_026752.1:n.347G>C||YES|||");
Assert.NotNull(annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First();
Assert.NotNull(altAllele);
AssertUtilities.CheckRefSeqTranscriptCount(1, altAllele);
var transcript = altAllele.RefSeqTranscripts.FirstOrDefault();
Assert.NotNull(transcript);
// ReSharper disable once PossibleNullReferenceException
var observedConsequence = string.Join("&", transcript.Consequence);
const string expectedConsequence = "splice_region_variant&non_coding_transcript_exon_variant&non_coding_transcript_variant";
Assert.Equal(expectedConsequence, observedConsequence);
}
