/// <summary>
/// Left aligns the variant using base rotation
/// </summary>
/// <returns>Tuple of new position, ref and alt allele</returns>
public Tuple <int, string, string> LeftAlign(int refPosition, string refAllele, string altAllele)
{
var trimmedAllele = BiDirectionalTrimmer.Trim(refPosition, refAllele, altAllele);
var trimmedPos = trimmedAllele.Item1;
var trimmedRefAllele = trimmedAllele.Item2;
var trimmedAltAllele = trimmedAllele.Item3;
// alignment only makes sense for insertion and deletion
if (!(trimmedAltAllele.Length == 0 || trimmedRefAllele.Length == 0))
{
return(null);
}
var upstreamSeq = GetUpstreamSeq(trimmedPos, MaxRotationRange);
if (upstreamSeq == null)
{
throw new InvalidDataException("Reference sequence not set, please check that it is loaded");
}
// compressed seq is 0 based
var combinedSeq = upstreamSeq;
int repeatLength;
int i;
if (trimmedRefAllele.Length > trimmedAltAllele.Length)
{
// deletion
combinedSeq += trimmedRefAllele;
repeatLength = trimmedRefAllele.Length;
for (i = combinedSeq.Length - 1; i >= repeatLength; i--, trimmedPos--)
{
if (combinedSeq[i] != combinedSeq[i - repeatLength])
{
break;
}
}
var newRefAllele = combinedSeq.Substring(i + 1 - repeatLength, repeatLength);
return(Tuple.Create(trimmedPos, newRefAllele, "")); //alt is empty for deletion
}
else
{
//insertion
combinedSeq += trimmedAltAllele;
repeatLength = trimmedAltAllele.Length;
for (i = combinedSeq.Length - 1; i >= repeatLength; i--, trimmedPos--)
{
if (combinedSeq[i] != combinedSeq[i - repeatLength])
{
break;
}
}
var newAltAllele = combinedSeq.Substring(i + 1 - repeatLength, repeatLength);
return(Tuple.Create(trimmedPos, "", newAltAllele));
}
}
/// <summary>
/// Right aligns the variant using base rotation
/// </summary>
/// <returns>Tuple of new position, ref and alt allele</returns>
public Tuple <int, string, string> RightAlign(int refPosition, string refAllele, string altAllele)
{
var trimmedAllele = BiDirectionalTrimmer.Trim(refPosition, refAllele, altAllele);
var trimmedPos = trimmedAllele.Item1;
var trimmedRefAllele = trimmedAllele.Item2;
var trimmedAltAllele = trimmedAllele.Item3;
//alignment only makes sense for insertion and deletion
if (!(trimmedAltAllele.Length == 0 || trimmedRefAllele.Length == 0))
{
return(null);
}
var downStreamSeq = GetDownstreamSeq(trimmedPos, MaxRotationRange);
if (downStreamSeq == null)
{
throw new InvalidDataException("Reference sequence not set, please check that it is loaded");
}
string combinedSeq;
int repeatLength;
int i;
if (trimmedRefAllele.Length > trimmedAltAllele.Length)
{
// deletion
repeatLength = trimmedRefAllele.Length;
combinedSeq = downStreamSeq;
for (i = 0; i < combinedSeq.Length - repeatLength; i++, trimmedPos++)
{
if (combinedSeq[i] != combinedSeq[i + repeatLength])
{
break;
}
}
var newRefAllele = combinedSeq.Substring(i, repeatLength);
return(Tuple.Create(trimmedPos, newRefAllele, "")); //alt is empty for deletion
}
else
{
//insertion
combinedSeq = trimmedAltAllele + downStreamSeq;
repeatLength = trimmedAltAllele.Length;
for (i = 0; i < combinedSeq.Length - repeatLength; i++, trimmedPos++)
{
if (combinedSeq[i] != combinedSeq[i + repeatLength])
{
break;
}
}
var newAltAllele = combinedSeq.Substring(i, repeatLength);
return(Tuple.Create(trimmedPos, "", newAltAllele));
}
}
