/// <summary>
/// Comparing allele1 and allele2 with dbsnp reference allele to suggest the action for adjustment.
/// </summary>
/// <returns></returns>
public StrandAction SuggestAction()
{
StrandAction result;
if (this.Allele2[0] == this.DbsnpRefAllele)
{
result = StrandAction.None;
}
else if (this.Allele1 == this.DbsnpRefAllele)
{
result = StrandAction.Switch;
}
else if (SequenceUtils.GetComplementAllele(this.Allele2[0]) == this.DbsnpRefAllele)
{
result = StrandAction.Flip;
}
else if (SequenceUtils.GetComplementAllele(this.Allele1) == this.DbsnpRefAllele)
{
result = StrandAction.FlipSwitch;
}
else
{
result = StrandAction.Unknown;
}
return(result);
}
public bool IsSourceAllelesMatchedWithG1000()
{
if (this.G1000Allele1 == ' ')
{
return(false);
}
var comp1 = SequenceUtils.GetComplementAllele(this.G1000Allele1);
var comp2 = SequenceUtils.GetComplementAllele(this.G1000Allele2);
var plat1 = Allele1;
var plat2 = Allele2[0];
if (plat1 == this.G1000Allele1 && plat2 == this.G1000Allele2)
{
return(true);
}
if (plat1 == this.G1000Allele2 && plat2 == this.G1000Allele1)
{
return(true);
}
if (plat1 == comp1 && plat2 == comp2)
{
return(true);
}
if (plat1 == comp2 && plat2 == comp1)
{
return(true);
}
return(false);
}
public SingleNucleotidePolymorphism GetNotGsnapMismatch(string querySequence)
{
if (this.NumberOfMismatch == 0)
{
return(null);
}
var isPositiveStrand = this.Strand == '+';
var m = mismatch.Match(this.MismatchPositions);
if (!m.Success)
{
return(null);
}
var seq = isPositiveStrand ? querySequence : SequenceUtils.GetReversedSequence(querySequence);
var pos = int.Parse(m.Groups[1].Value);
var detectedChr = seq[pos];
var chr = m.Groups[2].Value.First();
chr = isPositiveStrand ? chr : SequenceUtils.GetComplementAllele(chr);
return(new SingleNucleotidePolymorphism(pos, chr, detectedChr));
}
public bool IsPlatformAllelesMatchedWithDatabase()
{
if (this.G1000Allele1 == ' ')
{
return(false);
}
var comp1 = SequenceUtils.GetComplementAllele(this.G1000Allele1);
var comp2 = SequenceUtils.GetComplementAllele(this.G1000Allele2);
foreach (var plat in Platforms.Values)
{
var plat1 = plat.Allele1.First();
var plat2 = plat.Allele2.First();
if (plat1 == this.G1000Allele1 && plat2 == this.G1000Allele2)
{
continue;
}
if (plat1 == this.G1000Allele2 && plat2 == this.G1000Allele1)
{
continue;
}
if (plat1 == comp1 && plat2 == comp2)
{
continue;
}
if (plat1 == comp2 && plat2 == comp1)
{
continue;
}
return(false);
}
return(true);
}
public bool IsCompementary()
{
var comp2 = SequenceUtils.GetComplementAllele(this.G1000Allele2);
return(this.G1000Allele1 == comp2);
}