public void IdentifyConflictingItems()
{
var sequence = new SimpleSequence(new string('A', VariantUtils.MaxUpstreamLength) + "TAAGCCAGCCAGCCAGCCAAGCTGGCCAAGCCAGACAGGCAGCCAAGCCAACCAAGACACCCAGGCAGCCAAGCCAGC", 16558315 - VariantUtils.MaxUpstreamLength);
var refNameToChrom = new Dictionary <string, IChromosome> {
{ "22", Chrom22 }
};
var sequenceProvider = new SimpleSequenceProvider(GenomeAssembly.GRCh38, sequence, refNameToChrom);
var gnomadReader = new GnomadReader(new StreamReader(GetConflictingItemsStream()), sequenceProvider);
var items = new List <ISupplementaryDataItem>();
foreach (GnomadItem item in gnomadReader.GetItems())
{
//item.Trim();
if (item.Position == 16558315)
{
items.Add(item);
}
}
items = SuppDataUtilities.RemoveConflictingAlleles(items, false);
//two if the items were removed as conflicting items
Assert.Equal(3, items.Count);
}
private static IEnumerable <ISupplementaryDataItem> GetConflictingGnomadItems()
{
var sequence = new SimpleSequence(new string('T', VariantUtils.MaxUpstreamLength) + "AAAGAAAGAAAG", 17467787 - 1 - VariantUtils.MaxUpstreamLength);
var sequenceProvider = new SimpleSequenceProvider(GenomeAssembly.GRCh38, sequence, ChromosomeUtilities.RefNameToChromosome);
var gnomadReader = new GnomadReader(new StreamReader(GetChr22_17467787_17467799_genome()), null, sequenceProvider);
return(gnomadReader.GetCombinedItems());
}
public void GetItems_test()
{
var sequence = new SimpleSequence(new string('A', VariantUtils.MaxUpstreamLength) + "TGTGTTGTTATTCTGTGTGCAT", 10114 - VariantUtils.MaxUpstreamLength);
var refNameToChrom = new Dictionary <string, IChromosome> {
{ "1", Chrom1 }
};
var sequenceProvider = new SimpleSequenceProvider(GenomeAssembly.GRCh38, sequence, refNameToChrom);
var gnomadReader = new GnomadReader(new StreamReader(GetGnomadStream()), sequenceProvider);
var items = gnomadReader.GetItems().ToList();
Assert.Equal(2, items.Count);
Assert.Equal("\"coverage\":218,\"failedFilter\":true,\"allAf\":0,\"allAn\":8734,\"allAc\":0,\"allHc\":0,\"afrAf\":0,\"afrAn\":2168,\"afrAc\":0,\"afrHc\":0,\"amrAf\":0,\"amrAn\":324,\"amrAc\":0,\"amrHc\":0,\"easAf\":0,\"easAn\":438,\"easAc\":0,\"easHc\":0,\"finAf\":0,\"finAn\":1296,\"finAc\":0,\"finHc\":0,\"nfeAf\":0,\"nfeAn\":4054,\"nfeAc\":0,\"nfeHc\":0,\"asjAf\":0,\"asjAn\":100,\"asjAc\":0,\"asjHc\":0,\"othAf\":0,\"othAn\":354,\"othAc\":0,\"othHc\":0", items[0].GetJsonString());
}
public void LeftShiftingItems()
{
var sequence = new SimpleSequence(new string('A', VariantUtils.MaxUpstreamLength) + "GCGCGC", 157100394 - 1 - VariantUtils.MaxUpstreamLength);
var refNameToChrom = new Dictionary <string, IChromosome> {
{ "6", new Chromosome("chr6", "6", 6) }
};
var sequenceProvider = new SimpleSequenceProvider(GenomeAssembly.GRCh38, sequence, refNameToChrom);
var gnomadReader = new GnomadReader(new StreamReader(GetShiftingItemsStream()), sequenceProvider);
var items = gnomadReader.GetItems().ToList();
Assert.Equal(3, items.Count);
Assert.Equal(157100397, items[0].Position);
Assert.Equal(157100397, items[1].Position);
Assert.Equal(157100397, items[2].Position);
}
public void CreateTsvs()
{
var benchMark = new Benchmark();
using (var writer = new GnomadTsvWriter(_version, _outputDirectory, _refProvider.GenomeAssembly, _refProvider, _sequencingDataType))
{
var count = 0;
foreach (var fileStreamReader in _streamReaders)
{
var reader = new GnomadReader(fileStreamReader, _refProvider.RefNameToChromosome);
TsvWriterUtilities.WriteSortedItems(reader.GetGnomadItems(), writer);
Console.WriteLine($"ingested {count++} file in " + benchMark.GetElapsedTime());
}
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("gnomAD", _version.Version, timeSpan);
}