/// <summary>
/// Extracts a splice AI item from the specified VCF line.
/// </summary>
/// <param name="vcfLine"></param>
/// <returns></returns>
private SpliceAiItem ExtractItem(string vcfLine)
{
var splitLine = vcfLine.Split('\t');
if (splitLine.Length < VcfCommon.InfoIndex + 1)
{
return(null);
}
var chromosomeName = splitLine[VcfCommon.ChromIndex];
if (!_sequenceProvider.RefNameToChromosome.ContainsKey(chromosomeName))
{
return(null);
}
var chromosome = _sequenceProvider.RefNameToChromosome[chromosomeName];
var position = int.Parse(splitLine[VcfCommon.PosIndex]);
var refAllele = splitLine[VcfCommon.RefIndex];
var altAllele = splitLine[VcfCommon.AltIndex];
if (altAllele.Contains(','))
{
throw new DataException($"multiple alt allele present for {chromosome}-{position}");
}
var start = position;
//skipping insertions/deletions that were shifted
if (VariantUtils.IsLeftShiftPossible(refAllele, altAllele))
{
return(null);
}
(start, refAllele, altAllele) = BiDirectionalTrimmer.Trim(start, refAllele, altAllele);
var end = start + refAllele.Length - 1;
var isSpliceAdjacent = _spliceIntervals[chromosome.Index].OverlapsAny(start, end);
ParseInfoField(splitLine[VcfCommon.InfoIndex]);
if (!HasSignificantScore() && !isSpliceAdjacent)
{
return(null);
}
Count++;
return(new SpliceAiItem(chromosome, start, refAllele, altAllele, _geneSymbol,
_acceptorGainScore, _acceptorLossScore, _donorGainScore, _donorLossScore,
_acceptorGainPosition, _acceptorLossPosition, _donorGainPosition, _donorLossPosition, isSpliceAdjacent));
}
public void CanNotLeftRotate(string refAllele, string altAllele, bool result)
{
Assert.Equal(result, VariantUtils.IsLeftShiftPossible(refAllele, altAllele));
}
