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 ExacExtraction()
{
const string vcfLine = "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";
var exacReader = new ExacReader(null, _refChromDict);
var exacItems = exacReader.ExtractItems(vcfLine);
var allAlleleNumber = exacItems[0].AllAlleleNumber;
var allAlleleCount = exacItems[0].AllAlleleCount;
var allAlleleNumber2 = exacItems[1].AllAlleleNumber;
var allAlleleCount2 = exacItems[1].AllAlleleCount;
Assert.NotNull(allAlleleNumber);
Assert.NotNull(allAlleleCount);
Assert.NotNull(allAlleleNumber2);
Assert.NotNull(allAlleleCount2);
Assert.Equal(10426, allAlleleNumber.Value);
Assert.Equal(28, exacItems[0].Coverage);
Assert.Equal("0.001247", (allAlleleCount.Value / (double)allAlleleNumber.Value).ToString(JsonCommon.FrequencyRoundingFormat));
Assert.Equal(10426, allAlleleNumber2.Value);
Assert.Equal(28, exacItems[1].Coverage);
Assert.Equal("0.000863", (allAlleleCount2.Value / (double)allAlleleNumber2.Value).ToString(JsonCommon.FrequencyRoundingFormat));
}
public void Merge1KgEvsExac()
{
const string vcfLine1 =
"1 13382 rs191719684 C G . PASS DBSNP=dbSNP_135;EA_AC=0,8600;AA_AC=17,4389;TAC=17,12989;MAF=0.0,0.3858,0.1307;GTS=GG,GC,CC;EA_GTC=0,0,4300;AA_GTC=0,17,2186;GTC=0,17,6486;DP=54;GL=SAMD11;CP=0.0;CG=1.5;AA=C;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_152486.2:intron;HGVS_CDNA_VAR=NM_152486.2:c.-30C>G;HGVS_PROTEIN_VAR=.;CDS_SIZES=NM_152486.2:2046;GS=.;PH=.;EA_AGE=.;AA_AGE=24.3+/-50.5";
const string vcfLine2 =
"1 13382 . C G 320.40 VQSRTrancheSNP99.60to99.80 AC=3;AC_AFR=0;AC_AMR=0;AC_Adj=1;AC_EAS=0;AC_FIN=0;AC_Het=1;AC_Hom=0;AC_NFE=0;AC_OTH=0;AC_SAS=1;AF=1.079e-04;AN=27810;AN_AFR=460;AN_AMR=82;AN_Adj=5728;AN_EAS=148;AN_FIN=4;AN_NFE=1400;AN_OTH=60;AN_SAS=3574;BaseQRankSum=-8.880e-01;ClippingRankSum=0.493;DP=86138;FS=0.000;GQ_MEAN=11.35;GQ_STDDEV=12.58;Het_AFR=0;Het_AMR=0;Het_EAS=0;Het_FIN=0;Het_NFE=0;Het_OTH=0;Het_SAS=1;Hom_AFR=0;Hom_AMR=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=0;InbreedingCoeff=-0.0832;MQ=34.49;MQ0=0;MQRankSum=-6.910e-01;NCC=72140;QD=20.03;ReadPosRankSum=-2.073e+00;VQSLOD=-4.106e+00;culprit=MQ;DP_HIST=9135|1821|1658|665|130|135|199|110|41|8|2|1|0|0|0|0|0|0|0|0,1|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=1432|8682|140|118|2625|254|121|17|3|1|10|24|364|94|9|11|0|0|0|0,0|1|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0;DOUBLETON_DIST=.;AC_MALE=1;AC_FEMALE=0;AN_MALE=3866;AN_FEMALE=1862;AC_CONSANGUINEOUS=0;AN_CONSANGUINEOUS=684;Hom_CONSANGUINEOUS=0";
const string vcfLine3 =
"1 13382 rs538606945 C G 100 PASS AC=1;AF=0.000199681;AN=5008;NS=2504;DP=28817;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001;AA=c|||;VT=SNP";
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(13382));
var evsReader = new EvsReader(_renamer);
var evsItem = evsReader.ExtractItems(vcfLine1)[0];
evsItem.SetSupplementaryAnnotations(sa1);
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(13382));
var exacReader = new ExacReader(_renamer);
var exacItem = exacReader.ExtractItems(vcfLine2)[0];
exacItem.SetSupplementaryAnnotations(sa2);
var sa3 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(13382));
var onekReader = new OneKGenReader(_renamer);
var onekItem = onekReader.ExtractItems(vcfLine3)[0];
onekItem.SetSupplementaryAnnotations(sa3);
sa1.MergeSaCreator(sa2);
sa1.MergeSaCreator(sa3);
var asa = sa1.SaPosition.AlleleSpecificAnnotations["G"];
var exac = asa.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var oneKg = asa.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)] as OneKGenAnnotation;
var evs = asa.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)] as EvsAnnotation;
Assert.NotNull(exac);
Assert.NotNull(oneKg);
Assert.NotNull(evs);
var oneKgAc = oneKg.OneKgAllAc;
var oneKgAn = oneKg.OneKgAllAn;
var exacAllAc = exac.ExacAllAc;
var exacAllAn = exac.ExacAllAn;
Assert.NotNull(oneKgAc);
Assert.NotNull(oneKgAn);
Assert.NotNull(exacAllAc);
Assert.NotNull(exacAllAn);
Assert.Equal("0.0002", (oneKgAc.Value / (double)oneKgAn.Value).ToString(JsonCommon.FrequencyRoundingFormat));
Assert.Equal("0.001307", evs.EvsAll);
Assert.Equal("0.000175", (exacAllAc.Value / (double)exacAllAn.Value).ToString(JsonCommon.FrequencyRoundingFormat));
}
private void CreateExacTsv(string fileName)
{
if (string.IsNullOrEmpty(fileName))
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
using (var writer = new ExacTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))))
{
var exacReader = new ExacReader(new FileInfo(fileName), _refNamesDictionary);
TsvWriterUtilities.WriteSortedItems(exacReader.GetExacItems(), writer);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("EXaC", version.Version, timeSpan);
}
public void ReadAndWriteExacWithMultipleAlleles()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var exacVersion = new DataSourceVersion("ExAC", "0.3.1", DateTime.Parse("2016-03-16").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
exacVersion
};
// create our expected supplementary annotations: note AN_adj is modified in this
const string vcfline =
"19 3121452 . TA T,TAA 17262.47 AC_Adj0_Filter AC=6,9;AC_AFR=0,0;AC_AMR=0,0;AC_Adj=0,0;AC_EAS=0,0;AC_FIN=0,0;AC_Het=0,0,0;AC_Hom=0,0;AC_NFE=0,0;AC_OTH=0,0;AC_SAS=0,0;AF=4.587e-03,6.881e-03;AN=1308;AN_AFR=0;AN_AMR=0;AN_Adj=3;AN_EAS=0;AN_FIN=0;AN_NFE=0;AN_OTH=0;AN_SAS=0;BaseQRankSum=0.437;DP=2838";
var sa = new SupplementaryAnnotationPosition(3121453);
var saCreator = new SupplementaryPositionCreator(sa);
var exacReader = new ExacReader(_renamer);
var additionalItems = new List <SupplementaryDataItem>();
foreach (var exacItem in exacReader.ExtractItems(vcfline))
{
var currentItem = exacItem.SetSupplementaryAnnotations(saCreator);
additionalItems.Add(currentItem);
}
var currentSa = new SupplementaryAnnotationPosition(3121453);
var currentSaCreator = new SupplementaryPositionCreator(currentSa);
foreach (var exacItem in additionalItems)
{
exacItem.SetSupplementaryAnnotations(currentSaCreator);
}
// write the supplementary annotation file
using (
var writer = new SupplementaryAnnotationWriter(randomPath, "chr19",
expectedDataSourceVersions))
{
writer.Write(currentSaCreator, currentSa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(3121453) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
// we want to make sure we are reading the values we have written
var expExaciA =
currentSa.AlleleSpecificAnnotations["iA"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(expExaciA);
var obsExaciA =
observedAnnotation1.AlleleSpecificAnnotations["iA"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(obsExaciA);
Assert.Equal(expExaciA.ExacAllAn, obsExaciA.ExacAllAn);
Assert.Equal(expExaciA.ExacCoverage, obsExaciA.ExacCoverage);
Assert.Equal(expExaciA.ExacAllAc, obsExaciA.ExacAllAc);
Assert.NotNull(obsExaciA.ExacAllAc);
Assert.Null(obsExaciA.ExacFinAc);
Assert.Null(obsExaciA.ExacFinAn);
// we want to make sure we are reading the values we have written
var expExac1 =
currentSa.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(expExac1);
var obsExac1 =
observedAnnotation1.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(obsExac1);
Assert.Equal(expExac1.ExacAllAn, obsExac1.ExacAllAn);
Assert.Equal(expExac1.ExacCoverage, obsExac1.ExacCoverage);
Assert.Equal(expExac1.ExacAllAc, obsExac1.ExacAllAc);
Assert.NotNull(obsExac1.ExacAllAc);
Assert.Null(obsExac1.ExacFinAc);
Assert.Null(obsExac1.ExacFinAn);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadWriteExacDbsnp()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var cosmicVersion = new DataSourceVersion("COSMIC", "GRCh37_v71", DateTime.Parse("2014-10-21").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, cosmicVersion
};
// create our expected supplementary annotations
const string vcfLine1 = "2 48010488 rs1042821 G A . . RS=1042821;RSPOS=48010488;RV;dbSNPBuildID=86;SSR=0;SAO=1;VP=0x050168420a05150136100100;GENEINFO=MSH6:2956;WGT=1;VC=SNV;PM;PMC;SLO;NSM;REF;U5;R5;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;LSD;CAF=0.7991,0.2009;COMMON=1";
const string vcfLine2 =
"2 48010488 rs1042821 G A,C 14068898.15 PASS AC=21019,1;AC_AFR=1700,0;AC_AMR=1015,1;AC_Adj=19510,1;AC_EAS=1973,0;AC_FIN=743,0;AC_Het=15722,1,0;AC_Hom=1894,0;AC_NFE=10593,0;AC_OTH=147,0;AC_SAS=3339,0;AF=0.178,8.487e-06;AN=117830;AN_AFR=6388;AN_AMR=9014;AN_Adj=91130;AN_EAS=6792;AN_FIN=5078;AN_NFE=48404;AN_OTH=664;AN_SAS=14790;BaseQRankSum=-4.850e-01;ClippingRankSum=-1.400e-01;DB;DP=1206681;FS=0.000;GQ_MEAN=129.86;GQ_STDDEV=221.88;Het_AFR=1322,0,0;Het_AMR=931,1,0;Het_EAS=1511,0,0;Het_FIN=665,0,0;Het_NFE=8585,0,0;Het_OTH=111,0,0;Het_SAS=2597,0,0;Hom_AFR=189,0;Hom_AMR=42,0;Hom_EAS=231,0;Hom_FIN=39,0;Hom_NFE=1004,0;Hom_OTH=18,0;Hom_SAS=371,0;InbreedingCoeff=0.0376;MQ=60.00;MQ0=0;MQRankSum=0.00;NCC=3737;POSITIVE_TRAIN_SITE;QD=17.46;ReadPosRankSum=0.181;VQSLOD=5.87;culprit=MQ;DP_HIST=3051|9435|11318|5521|9711|11342|4131|1270|615|404|328|266|264|262|196|186|126|115|97|277,133|968|2180|3402|3564|2815|1772|954|551|389|321|263|261|261|196|186|126|115|97|277,0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=949|2966|347|492|15135|1435|1335|854|421|526|590|416|13672|1951|445|462|255|174|211|16279,24|79|81|124|135|96|110|118|97|180|228|137|182|191|126|171|180|151|192|16229,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1";
var sa = new SupplementaryAnnotationPosition(48010488);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
dbSnpItem1.SetSupplementaryAnnotations(saCreator);
var exacReader = new ExacReader(_renamer);
foreach (var exacItem in exacReader.ExtractItems(vcfLine2))
{
exacItem.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr2", 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(48010488) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnpA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
var obsDbSnpA =
observedAnnotation1.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
Assert.NotNull(expDbSnpA);
Assert.NotNull(obsDbSnpA);
// we want to make sure we are reading the values we have written
Assert.Equal(expDbSnpA.DbSnp, obsDbSnpA.DbSnp);
var expExacA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var obsExacA =
observedAnnotation1.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
Assert.NotNull(expExacA);
Assert.NotNull(obsExacA);
Assert.Equal(expExacA.ExacAllAn, obsExacA.ExacAllAn);
Assert.Equal(expExacA.ExacCoverage, obsExacA.ExacCoverage);
Assert.Equal(Convert.ToDouble(expExacA.ExacAllAc), Convert.ToDouble(obsExacA.ExacAllAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacAfrAc), Convert.ToDouble(obsExacA.ExacAfrAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacAmrAc), Convert.ToDouble(obsExacA.ExacAmrAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacEasAc), Convert.ToDouble(obsExacA.ExacEasAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacFinAc), Convert.ToDouble(obsExacA.ExacFinAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacNfeAc), Convert.ToDouble(obsExacA.ExacNfeAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacOthAc), Convert.ToDouble(obsExacA.ExacOthAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacSasAc), Convert.ToDouble(obsExacA.ExacSasAc));
var expExacC =
sa.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var obsExacC =
observedAnnotation1.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
Assert.NotNull(expExacC);
Assert.NotNull(obsExacC);
Assert.Equal(expExacC.ExacCoverage, obsExacC.ExacCoverage);
Assert.Equal(Convert.ToDouble(expExacC.ExacAllAc), Convert.ToDouble(obsExacC.ExacAllAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacAfrAc), Convert.ToDouble(obsExacC.ExacAfrAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacAmrAc), Convert.ToDouble(obsExacC.ExacAmrAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacEasAc), Convert.ToDouble(obsExacC.ExacEasAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacFinAc), Convert.ToDouble(obsExacC.ExacFinAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacNfeAc), Convert.ToDouble(obsExacC.ExacNfeAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacOthAc), Convert.ToDouble(obsExacC.ExacOthAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacSasAc), Convert.ToDouble(obsExacC.ExacSasAc));
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
// constructor
public CreateSupplementaryDatabase(
string compressedReferencePath,
string nsdBaseFileName,
string dbSnpFileName = null,
string cosmicVcfFile = null,
string cosmicTsvFile = null,
string clinVarFileName = null,
string oneKGenomeAfFileName = null,
string evsFileName = null,
string exacFileName = null,
List <string> customFiles = null,
string dgvFileName = null,
string oneKSvFileName = null,
string clinGenFileName = null,
string chrWhiteList = null)
{
_nsdBaseFileName = nsdBaseFileName;
_dataSources = new List <DataSourceVersion>();
_iSupplementaryDataItemList = new List <IEnumerator <SupplementaryDataItem> >();
_supplementaryIntervalList = new List <SupplementaryInterval>();
Console.WriteLine("Creating supplementary annotation files... Data version: {0}, schema version: {1}", SupplementaryAnnotationCommon.DataVersion, SupplementaryAnnotationCommon.SchemaVersion);
_compressedSequence = new CompressedSequence();
var compressedSequenceReader = new CompressedSequenceReader(FileUtilities.GetReadStream(compressedReferencePath), _compressedSequence);
_renamer = _compressedSequence.Renamer;
_dataFileManager = new DataFileManager(compressedSequenceReader, _compressedSequence);
if (!string.IsNullOrEmpty(chrWhiteList))
{
Console.WriteLine("Creating SA for the following chromosomes only:");
foreach (var refSeq in chrWhiteList.Split(','))
{
InputFileParserUtilities.ChromosomeWhiteList.Add(_renamer.GetEnsemblReferenceName(refSeq));
Console.Write(refSeq + ",");
}
Console.WriteLine();
}
else
{
InputFileParserUtilities.ChromosomeWhiteList = null;
}
if (dbSnpFileName != null)
{
AddSourceVersion(dbSnpFileName);
var dbSnpReader = new DbSnpReader(new FileInfo(dbSnpFileName), _renamer);
var dbSnpEnumerator = dbSnpReader.GetEnumerator();
_iSupplementaryDataItemList.Add(dbSnpEnumerator);
}
if (cosmicVcfFile != null && cosmicTsvFile != null)
{
AddSourceVersion(cosmicVcfFile);
var cosmicReader = new MergedCosmicReader(cosmicVcfFile, cosmicTsvFile, _renamer);
var cosmicEnumerator = cosmicReader.GetEnumerator();
_iSupplementaryDataItemList.Add(cosmicEnumerator);
}
if (oneKGenomeAfFileName != null)
{
AddSourceVersion(oneKGenomeAfFileName);
var oneKGenReader = new OneKGenReader(new FileInfo(oneKGenomeAfFileName), _renamer);
var oneKGenEnumerator = oneKGenReader.GetEnumerator();
_iSupplementaryDataItemList.Add(oneKGenEnumerator);
}
if (oneKSvFileName != null)
{
if (oneKGenomeAfFileName == null)
{
AddSourceVersion(oneKSvFileName);
}
var oneKGenSvReader = new OneKGenSvReader(new FileInfo(oneKSvFileName), _renamer);
var oneKGenSvEnumerator = oneKGenSvReader.GetEnumerator();
_iSupplementaryDataItemList.Add(oneKGenSvEnumerator);
}
if (evsFileName != null)
{
AddSourceVersion(evsFileName);
var evsReader = new EvsReader(new FileInfo(evsFileName), _renamer);
var evsEnumerator = evsReader.GetEnumerator();
_iSupplementaryDataItemList.Add(evsEnumerator);
}
if (exacFileName != null)
{
AddSourceVersion(exacFileName);
var exacReader = new ExacReader(new FileInfo(exacFileName), _renamer);
var exacEnumerator = exacReader.GetEnumerator();
_iSupplementaryDataItemList.Add(exacEnumerator);
}
if (clinVarFileName != null)
{
AddSourceVersion(clinVarFileName);
var clinVarReader = new ClinVarXmlReader(new FileInfo(clinVarFileName), compressedSequenceReader, _compressedSequence);
var clinVarList = clinVarReader.ToList();
clinVarList.Sort();
Console.WriteLine($"{clinVarList.Count} clinvar items read form XML file");
IEnumerator <ClinVarItem> clinVarEnumerator = clinVarList.GetEnumerator();
_iSupplementaryDataItemList.Add(clinVarEnumerator);
}
if (dgvFileName != null)
{
AddSourceVersion(dgvFileName);
var dgvReader = new DgvReader(new FileInfo(dgvFileName), _renamer);
var dgvEnumerator = dgvReader.GetEnumerator();
_iSupplementaryDataItemList.Add(dgvEnumerator);
}
if (clinGenFileName != null)
{
AddSourceVersion(clinGenFileName);
var clinGenReader = new ClinGenReader(new FileInfo(clinGenFileName), _renamer);
var clinGenEnumerator = clinGenReader.GetEnumerator();
_iSupplementaryDataItemList.Add(clinGenEnumerator);
}
if (customFiles != null)
{
foreach (var customFile in customFiles)
{
AddSourceVersion(customFile);
var customReader = new CustomAnnotationReader(new FileInfo(customFile), _renamer);
var customEnumerator = customReader.GetEnumerator();
_iSupplementaryDataItemList.Add(customEnumerator);
}
}
// initializing the IEnumerators in the list
foreach (var iDataEnumerator in _iSupplementaryDataItemList)
{
if (!iDataEnumerator.MoveNext())
{
_iSupplementaryDataItemList.Remove(iDataEnumerator);
}
}
_additionalItemsList = new List <SupplementaryDataItem>();
}
