/// <summary>
/// Gets the reference sequence alignment length depending on the CIGAR value.
/// </summary>
/// <returns>Length of the alignment.</returns>
private int GetRefSeqAlignmentLengthFromCIGAR()
{
if (string.IsNullOrWhiteSpace(CIGAR) || CIGAR.Equals("*"))
{
return(DefaultReadLength);
}
var elements = CigarUtils.GetCigarElements(CIGAR);
int len = 0;
foreach (var v in elements)
{
if (CigarUtils.CigarElementis_MDNX_Equal(v.Operation))
{
len += v.Length;
}
}
return(len);
}
public int?GetReadIndexOfAlignmentPosition(int referencePosition)
{
if (string.IsNullOrWhiteSpace(CIGAR) || CIGAR.Equals("*"))
{
return(null);
}
int curRef = this.Pos; //location on ref
int curQuery = 0; //location on query
if (curRef == referencePosition)
{
return(curQuery);
}
var elements = CigarUtils.GetCigarElements(CIGAR);
string CIGARforClen = "MDNX=";
foreach (var e in elements)
{
char ch = e.Operation;
if (ch == 'P' || ch == 'N')
{
throw new Exception("Not built to handle clipping yet");
}
int start = 0;
int end = 0;
int len;
if (CigarUtils.CigarElementis_MDNX_Equal(ch))
{
len = e.Length;
bool addRef = false;
bool addQuery = false;
if (ch == 'M' || ch == '=' || ch == 'X')
{
addRef = true;
addQuery = true;
}
else if (ch == 'D')
{
addRef = true;
}
else if (ch == 'I' || ch == 'S' || ch == 'H')
{
addQuery = true;
}
for (int j = 0; j < len; j++)
{
if (addRef)
{
curRef++;
}
if (addQuery)
{
curQuery++;
}
if (curRef == referencePosition && addQuery)
{
return(curQuery);
}
}
if (curRef > referencePosition)
{
return(null);
}
}
}
return(null);
}