// make sure individual read cigars make sense against stitched cigar
protected static void ValidateCigar(CigarAlignment stitchedCigar, CigarAlignment read1Cigar, CigarAlignment read2Cigar)
{
if (!stitchedCigar.IsSupported())
{
throw new Exception(String.Format("Unsupported cigar: {0}", stitchedCigar));
}
ValidateCigar(stitchedCigar, read1Cigar);
ValidateCigar(stitchedCigar.GetReverse(), read2Cigar.GetReverse());
}
// 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);
}