private static void AssignExtended(string transcriptReferenceAllele, string transcriptAlternateAllele,
NullableInterval cdsInterval, NullableInterval proteinInterval, ISequence codingSequence, out string refCodons, out string altCodons)
{
refCodons = null;
altCodons = null;
if (cdsInterval.Start == null || cdsInterval.End == null || proteinInterval.Start == null ||
proteinInterval.End == null)
{
return;
}
int aminoAcidStart = proteinInterval.Start.Value * 3 - 2;
int aminoAcidEnd = proteinInterval.End.Value * 3;
int prefixLen = cdsInterval.Start.Value - aminoAcidStart;
int suffixLen = aminoAcidEnd - cdsInterval.End.Value;
int start1 = aminoAcidStart - 1;
int start2 = aminoAcidEnd - suffixLen;
int maxSuffixLen = codingSequence.Length - start2;
var atTailEnd = false;
if (suffixLen > maxSuffixLen)
{
suffixLen = maxSuffixLen;
atTailEnd = true;
}
if (suffixLen > maxSuffixLen)
{
suffixLen = maxSuffixLen;
}
string prefix = start1 + prefixLen < codingSequence.Length
? codingSequence.Substring(start1, prefixLen).ToLower()
: "AAA";
string suffix = suffixLen > 0
? codingSequence.Substring(start2, suffixLen).ToLower()
: "";
var needExtend = !atTailEnd && !Codons.IsTriplet(prefixLen + suffixLen + transcriptAlternateAllele.Length);
var extendedLen = (maxSuffixLen - suffixLen) > 45 ? 45 : (maxSuffixLen - suffixLen) / 3 * 3;
if (needExtend)
{
suffix = codingSequence.Substring(start2, suffixLen + extendedLen);
}
refCodons = Codons.GetCodon(transcriptReferenceAllele, prefix, suffix);
altCodons = Codons.GetCodon(transcriptAlternateAllele, prefix, suffix);
}
/// <summary>
/// returns true if the variant is a frameshift variant [VariantEffect.pm:940 frameshift]
/// </summary>
public bool IsFrameshiftVariant()
{
const ConsequenceType ct = ConsequenceType.FrameshiftVariant;
if (_cache.Contains(ct))
{
return(_cache.Get(ct));
}
// check the predicates
if (!_preCache.IsCoding)
{
_cache.Add(ct, false);
return(false);
}
bool result = false;
if (!_altAllele.IsStructuralVariant)
{
if (IsIncompleteTerminalCodonVariant() || !_ta.HasValidCdsStart || !_ta.HasValidCdsEnd)
{
_cache.Add(ct, false);
return(false);
}
int varLen = _ta.CodingDnaSequenceEnd - _ta.CodingDnaSequenceBegin + 1;
int alleleLen = _altAllele.AlternateAllele?.Length ?? 0;
result = !Codons.IsTriplet(alleleLen - varLen) && !IsStopRetained();
}
result = result && !IsTruncatedByStop();
_cache.Add(ct, result);
return(result);
}
public void IsTriplet(int len, bool expectedResult)
{
var observedResult = Codons.IsTriplet(len);
Assert.Equal(expectedResult, observedResult);
}
