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);
}
public void HasSoftclips()
{
var cigar = new CigarAlignment("1S5M");
Assert.True(cigar.HasSoftclips);
cigar = new CigarAlignment("5M1S");
Assert.True(cigar.HasSoftclips);
cigar = new CigarAlignment("5M");
Assert.False(cigar.HasSoftclips);
cigar.Add(new CigarOp('S', 1));
Assert.True(cigar.HasSoftclips);
cigar.Clear();
Assert.False(cigar.HasSoftclips);
cigar.Add(new CigarOp('S', 1));
Assert.True(cigar.HasSoftclips);
}
public void HasIndels()
{
var cigar = new CigarAlignment("1M1I5M");
Assert.True(cigar.HasIndels);
cigar = new CigarAlignment("1M1D5M");
Assert.True(cigar.HasIndels);
cigar = new CigarAlignment("5M");
Assert.False(cigar.HasIndels);
cigar.Add(new CigarOp('I', 1));
Assert.True(cigar.HasIndels);
cigar.Clear();
Assert.False(cigar.HasIndels);
cigar.Add(new CigarOp('I', 1));
Assert.True(cigar.HasIndels);
}
public static CigarAlignment GetClippedCigar(this CigarAlignment cigar, int start, int end, bool includeEndDels = true, bool includeWholeEndIns = false)
{
var numBases = 0;
var sourceCigar = cigar;
var readCycles = end - start;
var trimmedCigar = new CigarAlignment();
var prefixDels = new CigarAlignment();
bool lastWasDeletion = false;
if (readCycles > 0)
{
for (var i = 0; i < sourceCigar.Count; i++)
{
var operation = sourceCigar[i];
if (operation.IsReadSpan() && numBases + operation.Length - 1 < start)
{
lastWasDeletion = false;
numBases += (int)operation.Length;
continue;
}
if (!operation.IsReadSpan())
{
if (prefixDels.Count > 0 && !lastWasDeletion)
{
prefixDels.Clear();
}
if (trimmedCigar.Count == 0 && includeEndDels)
{
prefixDels.Add(operation);
}
if (trimmedCigar.Count > 0 && (numBases < readCycles || includeEndDels))
{
trimmedCigar.Add(operation); // doesn't contribute any read cycles (e.g. deletion), just add
}
}
else if (operation.Length + numBases <= end)
{
if (lastWasDeletion && prefixDels.Count > 0)
{
foreach (CigarOp prefixDel in prefixDels)
{
trimmedCigar.Add(prefixDel);
}
}
trimmedCigar.Add(operation);
numBases += (int)operation.Length;
}
else
{
if (lastWasDeletion && prefixDels.Count > 0)
{
foreach (CigarOp prefixDel in prefixDels)
{
trimmedCigar.Add(prefixDel);
}
}
if (end - numBases > 0)
{
if (includeWholeEndIns && operation.Type == 'I')
{
trimmedCigar.Add(new CigarOp(operation.Type, operation.Length));
}
else
{
trimmedCigar.Add(new CigarOp(operation.Type, (uint)(end - numBases)));
}
}
break;
}
lastWasDeletion = operation.Type == 'D';
}
}
//for (var i = 0; i < sourceCigar.Count; i++)
//{
// if (numBases >= end)
// {
// break;
// }
// var operation = sourceCigar[i];
// if (!operation.IsReadSpan())
// {
// if (numBases >= start && numBases <= end || includeEndDels)
// trimmedCigar.Add(operation); // doesn't contribute any read cycles (e.g. deletion), just add
// continue;
// }
// if (operation.Length + numBases >= end)
// {
// if (end - numBases > 0)
// trimmedCigar.Add(new CigarOp(operation.Type, (uint)(end - numBases - start)));
// //break;
// }
// else
// {
// if (operation.Length + numBases >= start)
// {
// trimmedCigar.Add(operation);
// }
// }
// if (operation.IsReadSpan())
// {
// numBases += (int)operation.Length;
// }
//}
trimmedCigar.Compress();
return(trimmedCigar);
}