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);
}
public void RemoveConflictingAlleles_does_not_remove_duplicates()
{
var seqProvider = ParserTestUtils.GetSequenceProvider(70220313, "TGCC", 'A', _chromDict);
var topMedReader = new TopMedReader(new StreamReader(GetDupItemsStream()), seqProvider);
var items = topMedReader.GetItems().ToList();
var saItems = new List <ISupplementaryDataItem>(items);
saItems = SuppDataUtilities.RemoveConflictingAlleles(saItems, false);
Assert.Single(saItems);
}
private void WritePosition(List <ISupplementaryDataItem> items)
{
int position = items[0].Position;
_memStream.Position = 0;
if (_isPositional)
{
var positionalItem = SuppDataUtilities.GetPositionalAnnotation(items);
if (positionalItem == null)
{
return;
}
_memWriter.Write(positionalItem.GetJsonString());
}
else
{
// any data source that is reported by allele and is not an array (e.g. allele frequencies) need this filtering step
if (_index.MatchByAllele && !_index.IsArray)
{
items = SuppDataUtilities.RemoveConflictingAlleles(items, _throwErrorOnConflicts);
}
if (_index.JsonKey == SaCommon.PrimateAiTag)
{
items = SuppDataUtilities.DeDuplicatePrimateAiItems(items);
}
_memWriter.WriteOpt(items.Count);
foreach (ISupplementaryDataItem saItem in items)
{
_memWriter.WriteOptAscii(saItem.RefAllele);
_memWriter.WriteOptAscii(saItem.AltAllele);
_memWriter.Write(saItem.GetJsonString());
}
}
int numBytes = (int)_memStream.Position;
if (!_block.HasSpace(numBytes))
{
Flush(items[0].Chromosome.Index);
}
_block.Add(_memBuffer, numBytes, position);
}
private static (Dictionary <(string refAllele, string altAllele), GnomadItem> genomeItems, Dictionary <(string refAllele, string altAllele), GnomadItem> exomeItems) GetMinItems(MinHeap <GnomadItem> minHeap)
{
var genomeItems = new List <ISupplementaryDataItem>();
var exomeItems = new List <ISupplementaryDataItem>();
if (minHeap.Count() == 0)
{
return(null, null);
}
var position = minHeap.GetMin().Position;
while (minHeap.Count() > 0 && minHeap.GetMin().Position == position)
{
var item = minHeap.ExtractMin();
if (item.DataType == GnomadDataType.Genome)
{
genomeItems.Add(item);
}
else
{
exomeItems.Add(item);
}
}
genomeItems = SuppDataUtilities.RemoveConflictingAlleles(genomeItems, false);
exomeItems = SuppDataUtilities.RemoveConflictingAlleles(exomeItems, false);
var genomeItemsByAllele = new Dictionary <(string refAllele, string altAllele), GnomadItem>();
foreach (var item in genomeItems)
{
genomeItemsByAllele.Add((item.RefAllele, item.AltAllele), (GnomadItem)item);
}
var exomeItemsByAllele = new Dictionary <(string refAllele, string altAllele), GnomadItem>();
foreach (var item in exomeItems)
{
exomeItemsByAllele.Add((item.RefAllele, item.AltAllele), (GnomadItem)item);
}
return(genomeItemsByAllele, exomeItemsByAllele);
}
