/// <summary>
/// Gets the reference sequence alignment length depending on the CIGAR value.
/// </summary>
/// <returns>Length of the alignment.</returns>
private int GetRefSeqAlignmentLengthFromCIGAR()
{
const string CIGARforClen = "MDNX=";
if (string.IsNullOrWhiteSpace(CIGAR) || CIGAR.Equals("*"))
{
return(DefaultReadLength);
}
var charsAndPositions = new List <KeyValuePair <char, int> >();
for (int i = 0; i < CIGAR.Length; i++)
{
char ch = CIGAR[i];
if (Char.IsDigit(ch))
{
continue;
}
charsAndPositions.Add(new KeyValuePair <char, int>(ch, i));
}
int len = 0;
for (int i = 0; i < charsAndPositions.Count; i++)
{
char ch = charsAndPositions[i].Key;
if (CIGARforClen.Contains(ch))
{
int start = i == 0 ? 0 : charsAndPositions[i - 1].Value + 1;
int end = charsAndPositions[i].Value - start;
len += int.Parse(CIGAR.Substring(start, end), CultureInfo.InvariantCulture);
}
}
return(len);
}
/// <summary>
/// Gets the read sequence length depending on the CIGAR value.
/// </summary>
/// <returns>Length of the read.</returns>
private int GetReadLengthFromCIGAR()
{
if (string.IsNullOrWhiteSpace(CIGAR) || CIGAR.Equals("*"))
{
return(DefaultReadLength);
}
List <char> chars = new List <char>();
Dictionary <int, int> dic = new Dictionary <int, int>();
for (int i = 0; i < CIGAR.Length; i++)
{
char ch = CIGAR[i];
if (Char.IsDigit(ch))
{
continue;
}
chars.Add(ch);
dic.Add(chars.Count - 1, i);
}
string CIGARforClen = "MDN";
int len = 0;
for (int i = 0; i < chars.Count; i++)
{
char ch = chars[i];
int start = 0;
int end = 0;
if (CIGARforClen.Contains(ch))
{
if (i == 0)
{
start = 0;
}
else
{
start = dic[i - 1] + 1;
}
end = dic[i] - start;
len += int.Parse(CIGAR.Substring(start, end), CultureInfo.InvariantCulture);
}
}
return(len);
}
/// <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);
}
