public void EvsOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
121913237
}
};
var evs = new EvsAnnotation
{
EvsAll = "0.0001",
EvsCoverage = "102",
NumEvsSamples = "3456"
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.Evs, "C", evs);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "EVS=0.0001|102|3456", VcfCommon.InfoIndex);
}
public void AlleleFrequency1KgOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var oneKg = new OneKGenAnnotation
{
OneKgAllAn = 5008,
OneKgAllAc = 2130,
OneKgAmrAn = 694,
OneKgAmrAc = 250
};
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
11554290
}
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "C", oneKg);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "AF1000G=0.425319", VcfCommon.InfoIndex);
}
public void OneAlleleFreqMissing()
{
var sa = new SupplementaryAnnotationPosition(825069);
var saCreator = new SupplementaryPositionCreator(sa);
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
4475692
}
};
var oneKg = new OneKGenAnnotation
{
OneKgAllAn = 5008,
OneKgAllAc = 3392
};
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "C", oneKg);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1 825069 rs4475692 G A,C 362.00 LowGQX;HighDPFRatio SNVSB=-36.9;SNVHPOL=3 GT:GQ:GQX:DP:DPF:AD 1/2:4:0:52:38:8,11,33",
"AF1000G=.,0.677316", VcfCommon.InfoIndex);
}
public void CosmicOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var saCreator = new SupplementaryPositionCreator(sa);
var altAllele = "C";
var cosmicItem1 = new CosmicItem("chr1", 115256529, "COSM1000", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, 1,
altAllele);
var cosmicItem2 = new CosmicItem("chr1", 115256529, "COSM1001", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, 1,
altAllele);
cosmicItem1.AddCosmicToSa(saCreator);
cosmicItem2.AddCosmicToSa(saCreator);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "cosmic=1|COSM1000", VcfCommon.InfoIndex);
}
public void MergeSnvAndDeletion()
{
// NIR-906
const string vcfLine1 =
"1 862389 rs6693546 A G . . RS=6693546;RSPOS=862389;dbSNPBuildID=116;SSR=0;SAO=0;VP=0x05010008000515013e000100;WGT=1;VC=SNV;SLO;INT;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;CAF=0.3171,0.6829;COMMON=1";
const string vcfLine2 = "1 862388 rs534606253 GA G . . RS=534606253;RSPOS=862389;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000080005040024000200;WGT=1;VC=DIV;INT;ASP;VLD;KGPhase3;CAF=0.996,0.003994;COMMON=1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpEntry1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var dbSnpEntry2 = dbsnpReader.ExtractItem(vcfLine2)[0];
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(862389));
dbSnpEntry1.SetSupplementaryAnnotations(sa);
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(862389));
var additionalEntry = dbSnpEntry2.SetSupplementaryAnnotations(sa2);
additionalEntry.SetSupplementaryAnnotations(sa2);
sa.MergeSaCreator(sa2);
sa.FinalizePositionalAnnotations();
Assert.Equal("G", sa.SaPosition.GlobalMajorAllele);
Assert.Equal("0.6829", sa.SaPosition.GlobalMajorAlleleFrequency);
Assert.Equal("A", sa.SaPosition.GlobalMinorAllele);
Assert.Equal("0.3171", sa.SaPosition.GlobalMinorAlleleFrequency);
}
public void NumEvsSamplesTest()
{
const string vcfLine = "1 1564952 rs112177324 TG TGG,T . PASS BSNP=dbSNP_132;EA_AC=2,3039,4701;AA_AC=44,279,3231;TAC=46,3318,7932;MAF=39.2793,9.0884,29.7805;GTS=A1A1,A1A2,A1R,A2A2,A2R,RR;EA_GTC=0,1,1,707,1624,1538;AA_GTC=4,4,32,41,193,1503;GTC=4,5,33,748,1817,3041;DP=10;GL=MIB2;CP=0.8;CG=-0.0;AA=.;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_080875.2:intron,NM_080875.2:intron,NM_001170689.1:intron,NM_001170689.1:intron,NM_001170688.1:intron,NM_001170688.1:intron,NM_001170687.1:intron,NM_001170687.1:intron,NM_001170686.1:intron,NM_001170686.1:intron;HGVS_CDNA_VAR=NM_080875.2:c.2908+7del1,NM_080875.2:c.2908+6_2908+7insG,NM_001170689.1:c.2187-66del1,NM_001170689.1:c.2187-67_2187-66insG,NM_001170688.1:c.2713+7del1,NM_001170688.1:c.2713+6_2713+7insG,NM_001170687.1:c.2866+7del1,NM_001170687.1:c.2866+6_2866+7insG,NM_001170686.1:c.2896+7del1,NM_001170686.1:c.2896+6_28967insG;HGVS_PROTEIN_VAR=.,.,.,.,.,.,.,.,.,.;CDS_SIZES=NM_080875.2:3213,NM_080875.2:3213,NM_001170689.1:2262,NM_001170689.1:2262,NM_001170688.1:3018,NM_001170688.1:3018,NM_001170687.1:3171,NM_001170687.1:3171,NM_001170686.1:3201,NM_001170686.1:3201;GS=.,.,.,.,.,.,.,.,.,.;PH=.,.,.,.,.,.,.,.,.,.;EA_AGE=.;AA_AGE=.";
var evsReader = new EvsReader(_renamer);
var evsItemsList = evsReader.ExtractItems(vcfLine);
var sa = new SupplementaryAnnotationPosition(1564953);
var saCreator = new SupplementaryPositionCreator(sa);
var additionalItems = new List <SupplementaryDataItem>();
foreach (var evsItem in evsItemsList)
{
additionalItems.Add(evsItem.SetSupplementaryAnnotations(saCreator));
}
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(saCreator);
}
var evs =
sa.AlleleSpecificAnnotations["iG"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)] as EvsAnnotation;
Assert.NotNull(evs);
Assert.Equal("5648", evs.NumEvsSamples);//GTC=4,5,33,748,1817,3041;
}
public void MergeConflictingEvsItems()
{
const string vcfLine1 = "1 1564952 rs112177324 T G,A . PASS BSNP=dbSNP_132;EA_AC=2,3039,4701;AA_AC=44,279,3231;TAC=46,3318,7932;MAF=39.2793,9.0884,29.7805;GTS=A1A1,A1A2,A1R,A2A2,A2R,RR;EA_GTC=0,1,1,707,1624,1538;AA_GTC=4,4,32,41,193,1503;GTC=4,5,33,748,1817,3041;DP=10;GL=MIB2;CP=0.8;CG=-0.0;AA=.;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_080875.2:intron,NM_080875.2:intron,NM_001170689.1:intron,NM_001170689.1:intron,NM_001170688.1:intron,NM_001170688.1:intron,NM_001170687.1:intron,NM_001170687.1:intron,NM_001170686.1:intron,NM_001170686.1:intron;HGVS_CDNA_VAR=NM_080875.2:c.2908+7del1,NM_080875.2:c.2908+6_2908+7insG,NM_001170689.1:c.2187-66del1,NM_001170689.1:c.2187-67_2187-66insG,NM_001170688.1:c.2713+7del1,NM_001170688.1:c.2713+6_2713+7insG,NM_001170687.1:c.2866+7del1,NM_001170687.1:c.2866+6_2866+7insG,NM_001170686.1:c.2896+7del1,NM_001170686.1:c.2896+6_28967insG;HGVS_PROTEIN_VAR=.,.,.,.,.,.,.,.,.,.;CDS_SIZES=NM_080875.2:3213,NM_080875.2:3213,NM_001170689.1:2262,NM_001170689.1:2262,NM_001170688.1:3018,NM_001170688.1:3018,NM_001170687.1:3171,NM_001170687.1:3171,NM_001170686.1:3201,NM_001170686.1:3201;GS=.,.,.,.,.,.,.,.,.,.;PH=.,.,.,.,.,.,.,.,.,.;EA_AGE=.;AA_AGE=.";
const string vcfLine2 = "1 1564952 rs140739101 T A . PASS BSNP=dbSNP_134;EA_AC=313,6535;AA_AC=14,3808;TAC=327,10343;MAF=4.5707,0.3663,3.0647;GTS=GG,GT,TT;EA_GTC=92,129,3203;AA_GTC=1,12,1898;GTC=93,141,5101;DP=110;GL=OR4F5;CP=1.0;CG=0.9;AA=T;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001005484.1:missense;HGVS_CDNA_VAR=NM_001005484.1:c.338T>G;HGVS_PROTEIN_VAR=NM_001005484.1:p.(F113C);CDS_SIZES=NM_001005484.1:918;GS=205;PH=probably-damaging:0.999;EA_AGE=.;AA_AGE=.";
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(1564952));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(1564952));
var evsReader = new EvsReader(_renamer);
var evsItems = evsReader.ExtractItems(vcfLine1);
foreach (var item in evsItems)
{
item.SetSupplementaryAnnotations(sa1);
}
evsItems.Clear();
evsItems.AddRange(evsReader.ExtractItems(vcfLine2));
foreach (var item in evsItems)
{
item?.SetSupplementaryAnnotations(sa2);
}
sa1.MergeSaCreator(sa2);
var evs =
sa1.SaPosition.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)] as
EvsAnnotation;
Assert.NotNull(evs);
Assert.True(evs.HasConflicts);
}
public void MergeConflictingOneKitemsSnv()
{
const string vcfLine1 =
"X 129354240 rs1160681 C A 100 PASS AC=1996;AF=0.528742;AN=3775;NS=2504;DP=10421;AMR_AF=0.353;AFR_AF=0.5953;EUR_AF=0.3052;SAS_AF=0.3896;EAS_AF=0.2738;AA=C|||;VT=SNP";
const string vcfLine2 =
"X 129354240 . C A,G 100 PASS AC=1981,15;AF=0.524768,0.00397351;AN=3775;NS=2504;DP=10421;AMR_AF=0.353,0;AFR_AF=0.584,0.0113;EUR_AF=0.3052,0;SAS_AF=0.3896,0;EAS_AF=0.2738,0;AA=C|||;VT=SNP;MULTI_ALLELIC";
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(129354240));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(129354240));
var oneKitem1 = _oneKGenReader.ExtractItems(vcfLine1)[0];
oneKitem1.SetSupplementaryAnnotations(sa1);
foreach (var oneKitem in _oneKGenReader.ExtractItems(vcfLine2))
{
oneKitem.SetSupplementaryAnnotations(sa2);
}
sa1.MergeSaCreator(sa2);
var oneKg =
sa1.SaPosition.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)] as
OneKGenAnnotation;
Assert.NotNull(oneKg);
Assert.True(oneKg.HasConflicts);
}
public void MergeConflictingExacItems()
{
const string vcfLine1 = "1 13528 . C G,T 1771.54 VQSRTrancheSNP99.60to99.80 AC=21,11;AC_AFR=12,0;AC_AMR=1,0;AC_Adj=13,9;AC_EAS=0,0;AC_FIN=0,0;AC_Het=13,9,0;AC_Hom=0,0;AC_NFE=0,2;AC_OTH=0,0;AC_SAS=0,7;AF=6.036e-04,3.162e-04;AN=34792;AN_AFR=390;AN_AMR=116;AN_Adj=10426;AN_EAS=150;AN_FIN=8;AN_NFE=2614;AN_OTH=116;AN_SAS=7032;BaseQRankSum=1.23;ClippingRankSum=0.056;DP=144988;FS=0.000;GQ_MEAN=14.54;GQ_STDDEV=16.53;Het_AFR=12,0,0;Het_AMR=1,0,0;Het_EAS=0,0,0;Het_FIN=0,0,0;Het_NFE=0,2,0;Het_OTH=0,0,0;Het_SAS=0,7,0;Hom_AFR=0,0;Hom_AMR=0,0;Hom_EAS=0,0;Hom_FIN=0,0;Hom_NFE=0,0;Hom_OTH=0,0;Hom_SAS=0,0;InbreedingCoeff=0.0557;MQ=31.08;MQ0=0;MQRankSum=-5.410e-01;NCC=67387;QD=1.91;ReadPosRankSum=0.206;VQSLOD=-2.705e+00;culprit=MQ;DP_HIST=10573|1503|705|1265|2477|613|167|52|18|11|8|3|0|0|1|0|0|0|0|0,2|6|2|1|4|0|3|1|0|0|2|0|0|0|0|0|0|0|0|0,1|0|0|0|1|1|3|0|1|1|1|0|0|0|1|0|0|0|0|0;GQ_HIST=342|11195|83|56|3154|517|367|60|12|4|5|7|1373|180|15|16|1|0|1|8,0|0|1|0|1|0|3|1|0|1|2|0|1|2|0|1|1|0|1|6,0|1|0|0|1|1|0|0|1|0|0|1|1|1|1|0|0|0|0|2";
const string vcfLine2 =
"1 13528 . C T 334.33 VQSRTrancheSNP99.60to99.80 AC=2;AC_AFR=0;AC_AMR=0;AC_Adj=2;AC_EAS=0;AC_FIN=0;AC_Het=2;AC_Hom=0;AC_NFE=0;AC_OTH=0;AC_SAS=2;AF=5.957e-05;AN=33576;AN_AFR=392;AN_AMR=114;AN_Adj=10200;AN_EAS=146;AN_FIN=6;AN_NFE=2556;AN_OTH=110;AN_SAS=6876;BaseQRankSum=-1.988e+00;ClippingRankSum=0.525;DP=142450;FS=2.634;GQ_MEAN=14.30;GQ_STDDEV=15.90;Het_AFR=0;Het_AMR=0;Het_EAS=0;Het_FIN=0;Het_NFE=0;Het_OTH=0;Het_SAS=2;Hom_AFR=0;Hom_AMR=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=-0.0753;MQ=31.78;MQ0=0;MQRankSum=0.578;NCC=68350;QD=5.31;ReadPosRankSum=-5.730e-01;VQSLOD=-3.582e+00;culprit=MQ;DP_HIST=10108|1417|742|1238|2324|682|184|56|20|11|4|2|0|0|0|0|0|0|0|0,0|0|0|1|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0;GQ_HIST=335|10726|91|50|3215|542|410|67|10|3|1|6|1138|163|14|15|0|0|0|2,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;DOUBLETON_DIST=0.028857408061;AC_MALE=1;AC_FEMALE=1;AN_MALE=7294;AN_FEMALE=2906;AC_CONSANGUINEOUS=0;AN_CONSANGUINEOUS=1360;Hom_CONSANGUINEOUS=0;";
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(13528));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(13528));
var exacReader = new ExacReader(_renamer);
var exacItems = exacReader.ExtractItems(vcfLine1);
foreach (var item in exacItems)
{
item.SetSupplementaryAnnotations(sa1);
}
exacItems.Clear();
exacItems.AddRange(exacReader.ExtractItems(vcfLine2));
foreach (var item in exacItems)
{
item?.SetSupplementaryAnnotations(sa2);
}
sa1.MergeSaCreator(sa2);
var exac =
sa1.SaPosition.AlleleSpecificAnnotations["T"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(exac);
Assert.True(exac.HasConflicts);
}
public void MergeDbSnp1Kg()
{
//NIR-1262
const string vcfLine =
"1 825069 rs4475692 G A,C . . RS=4475692;RSPOS=825069;dbSNPBuildID=111;SSR=0;SAO=0;VP=0x050100000005170126000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;GNO;KGPhase3;CAF=0.3227,.,0.6773;COMMON=1";
const string vcfLine1Kg =
"1 825069 rs4475692 G C 100 PASS AC=3392;AF=0.677316;AN=5008;NS=2504;DP=22495;EAS_AF=0.754;AMR_AF=0.5692;AFR_AF=0.6127;EUR_AF=0.7286;SAS_AF=0.7096;AA=g|||;VT=SNP;EAS_AN=1008;EAS_AC=760;EUR_AN=1006;EUR_AC=733;AFR_AN=1322;AFR_AC=810;AMR_AN=694;AMR_AC=395;SAS_AN=978;SAS_AC=694\tGT";
var dbsnpReader = new DbSnpReader(_renamer);
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(825069));
foreach (var dbSnpEntry in dbsnpReader.ExtractItem(vcfLine))
{
dbSnpEntry.SetSupplementaryAnnotations(sa);
}
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(825069));
var onekgReader = new OneKGenReader(_renamer);
foreach (var onekgItem in onekgReader.ExtractItems(vcfLine1Kg))
{
onekgItem.SetSupplementaryAnnotations(sa1);
}
sa.MergeSaCreator(sa1);
sa.FinalizePositionalAnnotations();
Assert.Equal("C", sa.SaPosition.GlobalMajorAllele);
Assert.Equal("G", sa.SaPosition.GlobalMinorAllele);
}
public void AlleleFrequencyArbitration()
{
const string vcfLine1 = "4 170887158 rs34734657 GCAAAA G 100 PASS AC=2222;AF=0.44369;AN=5008;NS=2504;DP=30687;EAS_AF=0.0675;AMR_AF=0.5447;AFR_AF=0.6377;EUR_AF=0.5547;SAS_AF=0.3834;VT=INDEL";
const string vcfLine2 = "4 170887158 rs556076439;rs34734657 GCAAAA GCAAAACAAAA,G 100 PASS AC=69,650;AF=0.013778,0.129792;AN=5008;NS=2504;DP=30687;EAS_AF=0.0109,0.2331;AMR_AF=0.0331,0.0303;AFR_AF=0.0045,0.1165;EUR_AF=0.0209,0.0099;SAS_AF=0.0082,0.2352;VT=INDEL;MULTI_ALLELIC";
const string vcfLine3 =
"4 170887158 rs536596553 GCAAAACAAAACAAAA G 100 PASS AC=32;AF=0.00638978;AN=5008;NS=2504;DP=30687;EAS_AF=0;AMR_AF=0.0029;AFR_AF=0.0023;EUR_AF=0.0268;SAS_AF=0;VT=INDEL";
var sa1 = new SupplementaryPositionCreator();
var additionalItems = _oneKGenReader.ExtractItems(vcfLine1).Select(oneKitem => oneKitem.SetSupplementaryAnnotations(sa1)).ToList();
additionalItems.AddRange(_oneKGenReader.ExtractItems(vcfLine2).Select(oneKitem => oneKitem.SetSupplementaryAnnotations(sa1)));
additionalItems.AddRange(_oneKGenReader.ExtractItems(vcfLine3).Select(oneKitem => oneKitem.SetSupplementaryAnnotations(sa1)));
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa1);
}
var oneKg =
sa1.SaPosition.AlleleSpecificAnnotations["5"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)
] as OneKGenAnnotation;
Assert.NotNull(oneKg);
Assert.True(oneKg.HasConflicts);
Assert.Null(oneKg.OneKgAllAc);
}
private void CloseCurrentSaWriter()
{
if (_currentRefName == null)
{
return;
}
//write last SA item
if (!_prevSaCreator.IsEmpty())
{
_saWriter.Write(_prevSaCreator, _prevSaCreator.ReferencePosition);
_numSaWritten++;
}
// reset _prevSa
_prevSaCreator = null;
// write the intervals
_saWriter.SetIntervalList(_supplementaryIntervalList);
Console.WriteLine("No of intervals: {0}", _supplementaryIntervalList.Count);
_saWriter.Dispose();
double lookupsPerSecond;
Console.WriteLine("No of annotations : {0}", _numSaWritten);
Console.WriteLine("{0} supplementary annotations written - {1}", _numSaWritten,
_creationBench.GetElapsedIterationTime(_numSaWritten, "variants", out lookupsPerSecond));
Console.WriteLine("No of ref minor positions: {0}", _saWriter.RefMinorCount);
}
public void DeletionAndSnvMerge()
{
// NIR-906
const string vcfLine1 =
"2 193187631 rs774176075 TGTTG T . . RS=774176075;RSPOS=193187632;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP";
const string vcfLine2 = "2 193187632 rs2592266 G T . . RS=2592266;RSPOS=193187632;dbSNPBuildID=100;SSR=0;SAO=0;VP=0x050000000005150026000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase3;CAF=0.01937,0.9806;COMMON=1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpEntry1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var dbSnpEntry2 = dbsnpReader.ExtractItem(vcfLine2)[0];
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(193187632));
var additionalEntry = dbSnpEntry1.SetSupplementaryAnnotations(sa);
additionalEntry.SetSupplementaryAnnotations(sa);
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(193187632));
dbSnpEntry2.SetSupplementaryAnnotations(sa2);
sa.MergeSaCreator(sa2);
sa.FinalizePositionalAnnotations();
Assert.Equal("T", sa.SaPosition.GlobalMajorAllele);
Assert.Equal("0.9806", sa.SaPosition.GlobalMajorAlleleFrequency);
Assert.Equal("G", sa.SaPosition.GlobalMinorAllele);
Assert.Equal("0.01937", sa.SaPosition.GlobalMinorAlleleFrequency);
}
public void MergeDbSnp1KpEvsRefMinor()
{
const string vcfLine1 = "1 69428 rs140739101 T G . . RS=140739101;RSPOS=69428;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050200000a05140026000100;WGT=1;VC=SNV;S3D;NSM;REF;ASP;VLD;KGPhase3;CAF=0.981,0.01897;COMMON=1";
//vcf line is modified
const string vcfLine2 = "1 69428 rs140739101 T G 100 PASS AC=4956;AF=0.989617;AN=5008;NS=2504;DP=17611;EAS_AF=0.003;AMR_AF=0.036;AFR_AF=0.0015;EUR_AF=0.0497;SAS_AF=0.0153;AA=.|||;VT=SNP;EX_TARGET;EAS_AN=1008;EAS_AC=3;EUR_AN=1006;EUR_AC=50;AFR_AN=1322;AFR_AC=2;AMR_AN=694;AMR_AC=25;SAS_AN=978;SAS_AC=15";
const string vcfLine3 = "1 69428 rs140739101 T G . PASS BSNP=dbSNP_134;EA_AC=313,6535;AA_AC=14,3808;TAC=327,10343;MAF=4.5707,0.3663,3.0647;GTS=GG,GT,TT;EA_GTC=92,129,3203;AA_GTC=1,12,1898;GTC=93,141,5101;DP=110;GL=OR4F5;CP=1.0;CG=0.9;AA=T;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001005484.1:missense;HGVS_CDNA_VAR=NM_001005484.1:c.338T>G;HGVS_PROTEIN_VAR=NM_001005484.1:p.(F113C);CDS_SIZES=NM_001005484.1:918;GS=205;PH=probably-damaging:0.999;EA_AGE=.;AA_AGE=.";
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(69428));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem = dbsnpReader.ExtractItem(vcfLine1)[0];
dbSnpItem.SetSupplementaryAnnotations(sa);
var oneKGenItem = _oneKGenReader.ExtractItems(vcfLine2)[0];
oneKGenItem.SetSupplementaryAnnotations(sa);
var evsReader = new EvsReader(_renamer);
var evsItem = evsReader.ExtractItems(vcfLine3)[0];
evsItem.SetSupplementaryAnnotations(sa);
sa.FinalizePositionalAnnotations();
var dbSnp = sa.SaPosition.AlleleSpecificAnnotations["G"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
Assert.NotNull(dbSnp);
Assert.Equal(new List <long> {
140739101
}, dbSnp.DbSnp);
Assert.Equal(true, sa.SaPosition.IsRefMinorAllele);
}
public void MultipleDbsnpMerge()
{
// NIR-778, 805. The second dbSNP id is missing from the SA database.
const string vcfLine1 =
"17 3616153 rs34081014 C G . . RS=34081014;RSPOS=3616153;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x050000000005140136000100;WGT=1;VC=SNV;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.9297,0.07029;COMMON=1";
const string vcfLine2 =
"17 3616152 rs71362546 GCTG GCTT,GGTG . . RS=71362546;RSPOS=3616153;dbSNPBuildID=130;SSR=0;SAO=0;VP=0x050100000005000102000810;WGT=1;VC=MNV;SLO;ASP;GNO;NOC";
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(3616153));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(3616153));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var dbSnpItems = dbsnpReader.ExtractItem(vcfLine2);
dbSnpItem1.SetSupplementaryAnnotations(sa1);
var additionalItems = dbSnpItems.Select(dbSnpItem => dbSnpItem.SetSupplementaryAnnotations(sa1)).ToList();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa2);
}
sa1.MergeSaCreator(sa2);
var dbSnp =
sa1.SaPosition.AlleleSpecificAnnotations["G"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnp);
Assert.Equal(dbSnp.DbSnp, new List <long> {
34081014, 71362546
});
}
public void BadRefMinor2()
{
// NIR-1368
const string vcfLine1 =
"X 1389061 . A C 100 PASS AC=3235;AF=0.645966;AN=5008;NS=2504;DP=13425;AMR_AF=0.7262;AFR_AF=0.2504;EUR_AF=0.8827;SAS_AF=0.7955;EAS_AF=0.7282;AA=a|||;VT=SNP";
const string vcfLine2 =
"X 1389061 . A C,T 100 PASS AC=2120,1771;AF=0.423323,0.353634;AN=5008;NS=2504;DP=13425;AMR_AF=0.4625,0.2997;AFR_AF=0.087,0.5998;EUR_AF=0.6551,0.2306;SAS_AF=0.5859,0.2157;EAS_AF=0.4484,0.3244;AA=a|||;VT=SNP;MULTI_ALLELIC";
var sa1 = new SupplementaryPositionCreator();
var sa2 = new SupplementaryPositionCreator();
foreach (var oneKitem in _oneKGenReader.ExtractItems(vcfLine1))
{
oneKitem.SetSupplementaryAnnotations(sa1);
}
foreach (var oneKitem in _oneKGenReader.ExtractItems(vcfLine2))
{
oneKitem.SetSupplementaryAnnotations(sa2);
}
sa1.MergeSaCreator(sa2);
Assert.False(sa1.IsRefMinor());
}
public void PrioretizingSymbolicAllele4Svs()
{
const string vcfLine =
"X 101155257 rs373174489 GTGCAAAAGCTCTTTAGTTTAATTAGGTCTCAGCTATTTATCTTTGTTCTTAT G 100 PASS AN=3775;AC=1723;AF=0.456424;AA=;EAS_AN=764;EAS_AC=90;EAS_AF=0.1178;EUR_AN=766;EUR_AC=439;EUR_AF=0.5731;AFR_AN=1003;AFR_AC=839;AFR_AF=0.8365;AMR_AN=524;AMR_AC=180;AMR_AF=0.3435;SAS_AN=718;SAS_AC=175;SAS_AF=0.2437";
var oneKItems = _oneKGenReader.ExtractItems(vcfLine);
Assert.False(oneKItems[0].IsInterval);
var sa = new SupplementaryPositionCreator();
var additionalItems = new List <SupplementaryDataItem>
{
oneKItems[0].SetSupplementaryAnnotations(sa)
};
foreach (var oneKitem in additionalItems)
{
oneKitem.SetSupplementaryAnnotations(sa);
}
var oneKg = sa.SaPosition.AlleleSpecificAnnotations["52"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)] as OneKGenAnnotation;
Assert.Equal("0.456424", GetAlleleFrequency(oneKg?.OneKgAllAn, oneKg?.OneKgAllAc));
Assert.Equal("0.836491", GetAlleleFrequency(oneKg?.OneKgAfrAn, oneKg?.OneKgAfrAc));
Assert.Equal("0.343511", GetAlleleFrequency(oneKg?.OneKgAmrAn, oneKg?.OneKgAmrAc));
Assert.Equal("0.117801", GetAlleleFrequency(oneKg?.OneKgEasAn, oneKg?.OneKgEasAc));
Assert.Equal("0.573107", GetAlleleFrequency(oneKg?.OneKgEurAn, oneKg?.OneKgEurAc));
Assert.Equal("0.243733", GetAlleleFrequency(oneKg?.OneKgSasAn, oneKg?.OneKgSasAc));
}
public void MergeDbSnpClinVar()
{
const string vcfLine = "1 225592188 rs387906416 TAGAAGA CTTCTAG . . RS=387906416;RSPOS=225592188;RV;dbSNPBuildID=137;SSR=0;SAO=1;VP=0x050060000605000002110800;GENEINFO=LBR:3930;WGT=1;VC=MNV;PM;NSN;REF;ASP;LSD;OM";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItems = dbsnpReader.ExtractItem(vcfLine);
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(225592188));
foreach (var dbSnpItem in dbSnpItems)
{
dbSnpItem.SetSupplementaryAnnotations(sa);
}
var xmlReader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000087262.xml")), _reader, _sequence);
foreach (var clinVarItem in xmlReader)
{
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(225592188));
clinVarItem.SetSupplementaryAnnotations(sa1);
sa.MergeSaCreator(sa1);
}
Assert.Equal(1, sa.SaPosition.ClinVarItems.Count);
foreach (var clinVarEntry in sa.SaPosition.ClinVarItems)
{
Assert.Equal(clinVarEntry.ID, "RCV000087262.3");
Assert.Equal(clinVarEntry.MedGenIDs.First(), "C0030779");
Assert.Equal(clinVarEntry.Phenotypes.First(), "Pelger-Huët anomaly");
}
}
public void MultiVariantEntry()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000007484.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
switch (clinVarItem.Start)
{
case 8045031:
Assert.Equal("G", clinVarItem.ReferenceAllele);
Assert.Equal("A", clinVarItem.AltAllele);
break;
case 8021911:
Assert.Equal("GTGCTGGACGGTGTCCCT", clinVarItem.AltAllele);
var sa = new SupplementaryAnnotationPosition(clinVarItem.Start);
var saCreator = new SupplementaryPositionCreator(sa);
clinVarItem.SetSupplementaryAnnotations(saCreator);
Assert.Equal("iGTGCTGGACGGTGTCCCT", clinVarItem.SaAltAllele);
break;
default:
throw new InvalidDataException($"Unexpected clinvar item start point : {clinVarItem.Start}");
}
}
}
public void MultiAltAlleleTest()
{
var sa = new SupplementaryPositionCreator();
foreach (var oneKitem in _oneKGenReader.ExtractItems(VcfLine2))
{
oneKitem.SetSupplementaryAnnotations(sa);
}
var oneKgG =
sa.SaPosition.AlleleSpecificAnnotations["G"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]
as OneKGenAnnotation;
var oneKgT =
sa.SaPosition.AlleleSpecificAnnotations["T"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]
as OneKGenAnnotation;
Assert.NotNull(oneKgG);
Assert.NotNull(oneKgT);
Assert.Equal("0.347244", GetAlleleFrequency(oneKgG.OneKgAllAn, oneKgG.OneKgAllAc));
Assert.Equal("0.322995", GetAlleleFrequency(oneKgG.OneKgAfrAn, oneKgG.OneKgAfrAc));
Assert.Equal("0.275216", GetAlleleFrequency(oneKgG.OneKgAmrAn, oneKgG.OneKgAmrAc));
Assert.Equal("0.481151", GetAlleleFrequency(oneKgG.OneKgEasAn, oneKgG.OneKgEasAc));
Assert.Equal("0.292247", GetAlleleFrequency(oneKgG.OneKgEurAn, oneKgG.OneKgEurAc));
Assert.Equal("0.349693", GetAlleleFrequency(oneKgG.OneKgSasAn, oneKgG.OneKgSasAc));
Assert.Equal("0.640974", GetAlleleFrequency(oneKgT.OneKgAllAn, oneKgT.OneKgAllAc));
Assert.Equal("0.636914", GetAlleleFrequency(oneKgT.OneKgAfrAn, oneKgT.OneKgAfrAc));
Assert.Equal("0.720461", GetAlleleFrequency(oneKgT.OneKgAmrAn, oneKgT.OneKgAmrAc));
Assert.Equal("0.518849", GetAlleleFrequency(oneKgT.OneKgEasAn, oneKgT.OneKgEasAc));
Assert.Equal("0.707753", GetAlleleFrequency(oneKgT.OneKgEurAn, oneKgT.OneKgEurAc)); //double check this one: 0.7077535
Assert.Equal("0.647239", GetAlleleFrequency(oneKgT.OneKgSasAn, oneKgT.OneKgSasAc));
}
public void MergeConflictingOneKitems1()
{
const string vcfLine1 =
"1 20505705 rs35377696 C CTCTG,CTG,CTGTG 100 PASS AC=46,1513,152;AF=0.0091853,0.302117,0.0303514;AN=5008;NS=2504;DP=23578;EAS_AF=0,0.2718,0.0268;AMR_AF=0.0086,0.2939,0.0072;AFR_AF=0.0303,0.2693,0.0756;EUR_AF=0,0.3032,0.001;SAS_AF=0,0.3824,0.0194";
const string vcfLine2 =
"1 20505705 . C CTG 100 PASS AC=4;AF=0.000798722;AN=5008;NS=2504;DP=23578;EAS_AF=0.002;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0.001;SAS_AF=0";
//var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(20505706);
//var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(20505706);
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(20505706));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(20505706));
var additionalItems = _oneKGenReader.ExtractItems(vcfLine1).Select(oneKitem => oneKitem.SetSupplementaryAnnotations(sa1)).ToList();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa1);
}
additionalItems.Clear();
additionalItems.AddRange(_oneKGenReader.ExtractItems(vcfLine2).Select(oneKitem => oneKitem.SetSupplementaryAnnotations(sa2)));
foreach (var item in additionalItems)
{
item?.SetSupplementaryAnnotations(sa2);
}
sa1.MergeSaCreator(sa2);
Assert.True(sa1.SaPosition.AlleleSpecificAnnotations["iTG"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)].HasConflicts);
// Assert.Null(sa1.AlleleSpecificAnnotations["iTG"].OneKgAll);
}
public void DuplicateDbsnp()
{
// NIR-853: can't reproduce the problem at dbSnp parsing and merging.
const string vcfLine1 =
"1 8121167 rs34500567 C CAAT,CAATAATAAAATAATAATAATAAT,CAATAAT,CAAT . . RS=34500567;RSPOS=8121167;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP;CAF=0.9726,.,.,.,.,0.9726;COMMON=1";
const string vcfLine2 =
"1 8121167 rs566669620 C CAATAATAAAAT . . RS=566669620;RSPOS=8121175;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.9726,0.0007987;COMMON=1";
const string vcfLine3 =
"1 8121167 rs59792241 C CAAT,CAATAATAAAATAATAATAATAAT,CAATAAT,CAAT . . RS=59792241;RSPOS=8121205;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP;CAF=0.9726,.,.,.,.,0.9726;COMMON=1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItems1 = dbsnpReader.ExtractItem(vcfLine1);
var dbSnpItems2 = dbsnpReader.ExtractItem(vcfLine2);
var dbSnpItems3 = dbsnpReader.ExtractItem(vcfLine3);
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(8121168));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(8121168));
var sa3 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(8121168));
var additionalItems = dbSnpItems1.Select(dbSnpItem => dbSnpItem.SetSupplementaryAnnotations(sa1)).ToList();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa1);
}
additionalItems.Clear();
additionalItems.AddRange(dbSnpItems2.Select(dbSnpItem => dbSnpItem.SetSupplementaryAnnotations(sa2)));
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa2);
}
additionalItems.Clear();
foreach (var dbSnpItem in dbSnpItems3)
{
additionalItems.Add(dbSnpItem.SetSupplementaryAnnotations(sa3));
}
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa3);
}
sa1.MergeSaCreator(sa2);
sa1.MergeSaCreator(sa3);
var dbSnp =
sa1.SaPosition.AlleleSpecificAnnotations["iAAT"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnp);
Assert.Equal(2, dbSnp.DbSnp.Count);
Assert.Equal(34500567, dbSnp.DbSnp[0]);
Assert.Equal(59792241, dbSnp.DbSnp[1]);
}
private static bool IsSnv(string refAllele, string altAlleles)
{
if (!SupplementaryPositionCreator.IsSnv(refAllele))
{
return(false);
}
return(altAlleles.Split(',').All(SupplementaryPositionCreator.IsSnv));
}
public void RwDbsnpGlobalAlleles()
{
//NIR-1262
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "147", DateTime.Parse("2016-07-26").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion
};
const string vcfLine1 =
"2 141724543 rs112783784 A C,T . . RS=112783784;RSPOS=141724543;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050100080015140136000100;WGT=1;VC=SNV;SLO;INT;OTH;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.04113,0.9105,0.04832;COMMON=1";
const string vcfLine2 =
"2 141724543 rs4300776 A C . . RS=4300776;RSPOS=141724543;dbSNPBuildID=111;SSR=0;SAO=0;VP=0x050100080015000102000100;WGT=1;VC=SNV;SLO;INT;OTH;ASP;GNO;CAF=0.04113,0.9105;COMMON=1";
var sa = new SupplementaryAnnotationPosition(141724543);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
foreach (var dbSnpItem in dbsnpReader.ExtractItem(vcfLine1))
{
dbSnpItem.SetSupplementaryAnnotations(saCreator);
}
foreach (var dbSnpItem in dbsnpReader.ExtractItem(vcfLine2))
{
dbSnpItem.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
saCreator.FinalizePositionalAnnotations();
writer.Write(saCreator, sa.ReferencePosition);
}
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation = reader.GetAnnotation(141724543) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation);
Assert.Equal("C", observedAnnotation.GlobalMajorAllele);
Assert.Equal("0.9105", observedAnnotation.GlobalMajorAlleleFrequency);
Assert.Equal("T", observedAnnotation.GlobalMinorAllele);
Assert.Equal("0.04832", observedAnnotation.GlobalMinorAlleleFrequency);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void AllSuppAnnotOutputTest()
{
const string altAllele = "C";
var sa = new SupplementaryAnnotationPosition(115256529);
var oneKg = new OneKGenAnnotation
{
OneKgAllAn = 5008,
OneKgAllAc = 2130,
OneKgAmrAn = 694,
OneKgAmrAc = 250
};
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
11554290
}
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "C", oneKg);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var cosmicItem1 = new CosmicItem("chr1", 115256529, "COSM1000", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, 1,
altAllele);
var cosmicItem2 = new CosmicItem("chr1", 115256529, "COSM1001", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, 1,
altAllele);
cosmicItem1.AddCosmicToSa(saCreator);
cosmicItem2.AddCosmicToSa(saCreator);
var clinvarItem1 = new ClinVarItem(null, 0, null, altAllele, null, "RCV001",
null, null, new List <string> {
"ORPHA2462"
}, null, null, "other");
sa.ClinVarItems.Add(clinvarItem1);
var saReader = new MockSupplementaryAnnotationReader(sa);
var infoColumn = VcfUtilities.GetVcfColumn(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", VcfCommon.InfoIndex);
Assert.Contains("AF1000G=0.425319", infoColumn);
Assert.Contains("cosmic=1|COSM1000,1|COSM1001", infoColumn);
Assert.Contains("clinvar=1|other", infoColumn);
}
public void CheckSaAltAllele()
{
var customItem = new CustomItem("chr1", 100, "ATATA", "TTT", "test", "cust101", true, null, null);
var spc = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(100));
customItem.SetSupplementaryAnnotations(spc);
Assert.Equal("5TTT", spc.SaPosition.CustomItems[0].SaAltAllele);
}
public void MixedVariantType()
{
var oneKItem = _oneKGenReader.ExtractItems(VcfLine4)[1];
var sa = new SupplementaryPositionCreator();
oneKItem.SetSupplementaryAnnotations(sa);
Assert.False(sa.IsRefMinor());
}
public void ReadWriteCustomAnnotation()
{
var randomPath = GetRandomPath(true);
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var clinVarVersion = new DataSourceVersion("ClinVar", "13.5", DateTime.Parse("2015-01-19").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, clinVarVersion
};
var customFile = new FileInfo(Resources.TopPath("customCosmic.vcf"));
var customReader = new CustomAnnotationReader(customFile, _renamer);
// all items from this file should be of type cosmic.
var customItems = customReader.ToList();
var sa = new SupplementaryAnnotationPosition(69224);
var saCreator = new SupplementaryPositionCreator(sa);
foreach (var customItem in customItems)
{
// NOTE that the two custom items are for different position, but for the purpose of our test, this is not an issue.
customItem.SetSupplementaryAnnotations(saCreator);
}
// the above code was unit tested in MergeDbSnpClinVar()
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(69224);
Assert.NotNull(observedAnnotation1);
for (var i = 0; i < sa.CustomItems.Count; i++)
{
Assert.Equal(sa.CustomItems[i].Id, observedAnnotation1.CustomItems[i].Id);
Assert.Equal(sa.CustomItems[i].AnnotationType, observedAnnotation1.CustomItems[i].AnnotationType);
Assert.Equal(sa.CustomItems[i].IsAlleleSpecific, observedAnnotation1.CustomItems[i].IsAlleleSpecific);
Assert.True(sa.CustomItems[i].StringFields.SequenceEqual(observedAnnotation1.CustomItems[i].StringFields));
if (sa.CustomItems[i].BooleanFields.Count > 0)
{
Assert.True(sa.CustomItems[i].BooleanFields.SequenceEqual(observedAnnotation1.CustomItems[i].BooleanFields));
}
}
}
}
public void RefAlleleMinor()
{
var sa = new SupplementaryPositionCreator();
foreach (var oneKitem in _oneKGenReader.ExtractItems(VcfLine2))
{
oneKitem.SetSupplementaryAnnotations(sa);
}
sa.FinalizePositionalAnnotations();
Assert.Equal(sa.IsRefMinor(), true);
}
public void RefAlleleMajor()
{
var sa = new SupplementaryPositionCreator();
foreach (var oneKitem in _oneKGenReader.ExtractItems(VcfLine1))
{
oneKitem.SetSupplementaryAnnotations(sa);
}
Assert.False(sa.IsRefMinor());
}