/// <summary>
/// Matches DNA with the primer.
/// </summary>
/// <param name="sequence">The DNA to search for.</param>
/// <returns>A primer if found, or null if none is found.</returns>
public PrimerMatch Match(FastQSequence sequence)
{
var dna = sequence.Sequence;
for (int i = 0; i < (dna.Length - Primer.Length); i++)
{
int errorCount = 0;
for (int j = 0; j < Primer.Length; j++)
{
if (dna[i + j] != Primer[j])
{
errorCount++;
}
if (errorCount > ErrorBound)
{
break;
}
}
if (errorCount <= ErrorBound)
{
return(new PrimerMatch(i, errorCount));
}
}
return(null);
}
/// <summary>
/// Matches DNA with the primer.
/// </summary>
/// <param name="sequence">The DNA to search for.</param>
/// <returns>A primer if found, or null if none is found.</returns>
public bool TryMatch(FastQSequence sequence, out PrimerMatch result)
{
var dna = sequence.Sequence;
for (var i = 0; i < dna.Length - Primer.Length; i++)
{
var errorCount = 0;
for (var j = 0; j < Primer.Length; j++)
{
if (dna[i + j] != Primer[j])
{
errorCount++;
}
if (errorCount > ErrorBound)
{
break;
}
}
if (errorCount <= ErrorBound)
{
result = new PrimerMatch(i, errorCount);
return(true);
}
}
result = default;
return(false);
}
public PrimerResult(FastQSequence forward, FastQSequence reverse, PrimerScanner.PrimerMatch forwardMatch,
PrimerScanner.PrimerMatch reverseMatch, bool reversed)
{
Forward = forward;
Reverse = reverse;
ForwardMatch = forwardMatch;
ReverseMatch = reverseMatch;
Reversed = reversed;
}
public static bool TryFind <T>(FastQSequence h1, FastQSequence h2, T scanners, out PrimerResult result)
where T : IEnumerable <(PrimerScanner forward, PrimerScanner reverse)>
FindPrimer(FastQSequence h1, FastQSequence h2, List <(PrimerScanner forward, PrimerScanner reverse)> scanners)