public void GetHeaderOnly()
{
var readStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("Clinvar20150901.json.gz")), CompressionMode.Decompress);
var indexStream = ResourceUtilities.GetReadStream(Resources.TopPath("Clinvar20150901.json.gz.jsi"));
var outStream = new MemoryStream();
using (var writer = new StreamWriter(outStream, Encoding.UTF8, 512, true))
using (var qp = new QueryProcessor(new StreamReader(readStream), indexStream, writer))
{
qp.PrintHeaderOnly();
}
Assert.NotEqual(0, outStream.Length);
outStream.Position = 0;
using (var reader = new StreamReader(outStream))
{
string headerLine = reader.ReadToEnd();
Assert.Equal("{\"header\":{\"annotator\":\"Nirvana 2.0.9.0\",\"creationTime\":\"2018-04-30 17:17:23\",\"genomeAssembly\":\"GRCh37\",\"schemaVersion\":6,\"dataVersion\":\"91.26.45\",\"dataSources\":[{\"name\":\"VEP\",\"version\":\"91\",\"description\":\"Ensembl\",\"releaseDate\":\"2018-03-05\"},{\"name\":\"ClinVar\",\"version\":\"20180129\",\"description\":\"A freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence\",\"releaseDate\":\"2018-01-29\"},{\"name\":\"COSMIC\",\"version\":\"84\",\"description\":\"somatic mutation and related details and information relating to human cancers\",\"releaseDate\":\"2018-02-13\"},{\"name\":\"dbSNP\",\"version\":\"150\",\"description\":\"Identifiers for observed variants\",\"releaseDate\":\"2017-04-03\"},{\"name\":\"gnomAD_exome\",\"version\":\"2.0.2\",\"description\":\"Exome allele frequencies from Genome Aggregation Database (gnomAD)\",\"releaseDate\":\"2017-10-05\"},{\"name\":\"gnomAD\",\"version\":\"2.0.2\",\"description\":\"Whole genome allele frequencies from Genome Aggregation Database (gnomAD)\",\"releaseDate\":\"2017-10-05\"},{\"name\":\"MITOMAP\",\"version\":\"20180228\",\"description\":\"Small variants in the MITOMAP human mitochondrial genome database\",\"releaseDate\":\"2018-02-28\"},{\"name\":\"1000 Genomes Project\",\"version\":\"Phase 3 v5a\",\"description\":\"A public catalogue of human variation and genotype data\",\"releaseDate\":\"2013-05-27\"},{\"name\":\"TOPMed\",\"version\":\"freeze_5\",\"description\":\"Allele frequencies from TOPMed data lifted over using dbSNP ids.\",\"releaseDate\":\"2017-08-28\"},{\"name\":\"ClinGen\",\"version\":\"20160414\",\"releaseDate\":\"2016-04-14\"},{\"name\":\"DGV\",\"version\":\"20160515\",\"description\":\"Provides a comprehensive summary of structural variation in the human genome\",\"releaseDate\":\"2016-05-15\"},{\"name\":\"MITOMAP\",\"version\":\"20180228\",\"description\":\"Large structural variants in the MITOMAP human mitochondrial genome database\",\"releaseDate\":\"2018-02-28\"},{\"name\":\"ExAC\",\"version\":\"0.3.1\",\"description\":\"Gene scores from the ExAC project\",\"releaseDate\":\"2016-03-16\"},{\"name\":\"OMIM\",\"version\":\"20180213\",\"description\":\"An Online Catalog of Human Genes and Genetic Disorders\",\"releaseDate\":\"2018-02-13\"},{\"name\":\"phyloP\",\"version\":\"hg19\",\"description\":\"46 way conservation score between humans and 45 other vertebrates\",\"releaseDate\":\"2009-11-10\"}]}}\r\n", headerLine);
}
}