/// <summary>
/// initialize from SAM CIGAR string:
/// </summary>
public CigarAlignment(string cigarString)
: this()
{
if (String.IsNullOrEmpty(cigarString) || (cigarString == "*"))
{
return;
}
int head = 0;
for (int i = 0; i < cigarString.Length; ++i)
{
if (Char.IsDigit(cigarString, i))
{
continue;
}
if (!BamUtilities.ArrayContains(BamConstants.CigarTypes, cigarString[i]))
{
throw new InvalidDataException(string.Format("ERROR: Unexpected format in character {0} of CIGAR string: {1}",
(i + 1), cigarString));
}
var length = uint.Parse(cigarString.Substring(head, i - head));
var op = new CigarOp(cigarString[i], length);
_data.Add(op);
head = i + 1;
}
if (head != cigarString.Length)
{
throw new InvalidDataException(string.Format("ERROR: Unexpected format in CIGAR string: {0}", cigarString));
}
}
public override bool Equals(Object obj)
{
// If parameter is null return false.
if (obj == null)
{
return(false);
}
// Throws an exception if the cast fails.
CigarOp co = (CigarOp)obj;
// Return true if the fields match:
return((Type == co.Type) && (Length == co.Length));
}
/// <summary>
/// provide the total trailing soft-clip
/// </summary>
public uint GetSuffixClip()
{
uint length = 0;
for (int index = (_data.Count - 1); index >= 0; index--)
{
CigarOp op = _data[index];
if (op.Type == 'S')
{
length += op.Length;
}
else if (op.Type != 'H')
{
break;
}
}
return(length);
}
public override bool Equals(Object obj)
{
// If parameter is null return false.
if (obj == null)
{
return(false);
}
// If parameter cannot be cast to Point return false.
CigarOp co = (CigarOp)obj;
if (co == null)
{
return(false);
}
// Return true if the fields match:
return((Type == co.Type) && (Length == co.Length));
}
/// <summary>
/// if duplicated adjacent tags are present, reduce them to one copy,
/// also reduce adjacent insertion/deletion tags to a single pair
/// </summary>
/// <returns>true if cigar was altered by compression</returns>
public bool Compress()
{
for (int segmentIndex = 0; segmentIndex < _data.Count; ++segmentIndex)
{
if (_data[segmentIndex].Length == 0)
{
continue;
}
for (int j = (segmentIndex + 1); j < _data.Count; ++j)
{
if (_data[j].Length == 0)
{
continue;
}
if (_data[segmentIndex].Type != _data[j].Type)
{
break;
}
_data[segmentIndex] = new CigarOp(_data[segmentIndex].Type, _data[segmentIndex].Length + _data[j].Length);
_data[j] = new CigarOp(_data[j].Type, 0);
}
}
int insertIndex = -1;
int deleteIndex = -1;
for (int segmentIndex = 0; segmentIndex < _data.Count; ++segmentIndex)
{
if (_data[segmentIndex].Length == 0)
{
continue;
}
if (_data[segmentIndex].Type == 'I')
{
if (insertIndex >= 0 && deleteIndex >= 0)
{
_data[insertIndex] = new CigarOp(_data[insertIndex].Type, _data[insertIndex].Length + _data[segmentIndex].Length);
_data[segmentIndex] = new CigarOp(_data[segmentIndex].Type, 0);
}
if (insertIndex == -1)
{
insertIndex = segmentIndex;
}
}
else if (_data[segmentIndex].Type == 'D')
{
if (insertIndex >= 0 && deleteIndex >= 0)
{
_data[deleteIndex] = new CigarOp(_data[deleteIndex].Type, _data[deleteIndex].Length + _data[segmentIndex].Length);
_data[segmentIndex] = new CigarOp(_data[segmentIndex].Type, 0);
}
if (deleteIndex == -1)
{
deleteIndex = segmentIndex;
}
}
else
{
insertIndex = -1;
deleteIndex = -1;
}
}
int numberRemoved = _data.RemoveAll(op => (op.Length == 0));
return(numberRemoved != 0);
}
public void Add(CigarOp op)
{
_data.Add(op);
}
public void Insert(int index, CigarOp op)
{
_data.Insert(index, op);
}