public static CigarAlignment GetReverse(this CigarAlignment cigar)
{
var reverseCigar = new CigarAlignment(cigar);
reverseCigar.Reverse();
return(reverseCigar);
}
public static CigarAlignment GetReadCigarFromStitched(string stitchedCigar, int readLength, bool reverse)
{
var cigar = new CigarAlignment(stitchedCigar);
if (reverse)
{
cigar.Reverse();
}
var totalLengthSofar = 0;
var newCigar = new CigarAlignment();
for (var i = 0; i < cigar.Count; i++)
{
var operation = cigar[i];
if (operation.IsReadSpan())
{
if (totalLengthSofar + operation.Length > readLength)
{
newCigar.Add(new CigarOp(operation.Type, (uint)(readLength - totalLengthSofar)));
break;
}
newCigar.Add(operation);
totalLengthSofar += (int)operation.Length;
if (totalLengthSofar == readLength)
{
break;
}
}
else
{
newCigar.Add(operation);
}
}
if (reverse)
{
newCigar.Reverse();
}
return(newCigar);
}
public void CigarString_Manipulation_Tests()
{
var cigarstring = new CigarAlignment("7M3I2D1S11M2S");
Assert.Equal(6, cigarstring.Count);
Assert.Equal("7M3I2D1S11M2S", cigarstring.ToString());
cigarstring.Add(new CigarOp('M', 6));
Assert.Equal("7M3I2D1S11M2S6M", cigarstring.ToString());
Assert.Equal(7, cigarstring.Count);
cigarstring.Reverse();
Assert.Equal("6M2S11M1S2D3I7M", cigarstring.ToString());
Assert.Equal(7, cigarstring.Count);
cigarstring.Clear();
Assert.Equal("", cigarstring.ToString());
Assert.Equal(0, cigarstring.Count);
}
// trim a cigar string up to a specified read length, cigar operations that don't span a read are taken as is
public static CigarAlignment GetTrimmed(this CigarAlignment cigar, int readCycles, bool fromEnd = false, bool includeEndDels = true)
{
var numBases = 0;
var sourceCigar = fromEnd ? cigar.GetReverse() : cigar;
var trimmedCigar = new CigarAlignment();
if (readCycles > 0)
{
for (var i = 0; i < sourceCigar.Count; i++)
{
var operation = sourceCigar[i];
if (!operation.IsReadSpan())
{
if (numBases < readCycles || includeEndDels)
{
trimmedCigar.Add(operation); // doesn't contribute any read cycles (e.g. deletion), just add
}
}
else if (operation.Length + numBases <= readCycles)
{
trimmedCigar.Add(operation);
numBases += (int)operation.Length;
}
else
{
if (readCycles - numBases > 0)
{
trimmedCigar.Add(new CigarOp(operation.Type, (uint)(readCycles - numBases)));
}
break;
}
}
}
if (fromEnd)
{
trimmedCigar.Reverse();
}
return(trimmedCigar);
}