/// <summary>
/// Method throws an exception if sequence violates any assumption made by this class anywhere.
/// Avoids, separate checks within each method.
/// </summary>
/// <param name="seq"></param>
private void validateSequence(SAMAlignedSequence seq)
{
if (seq == null) {
throw new ArgumentNullException("seq");
}
if (String.IsNullOrEmpty(seq.RName) ||
seq.RefEndPos <= seq.Pos ||
String.IsNullOrEmpty(seq.CIGAR) ||
seq.CIGAR =="*" ||
!(seq.QuerySequence is QualitativeSequence) )
{
throw new ArgumentException("Tried to build a pileup with an invalid sequence. Sequence was:\n"+
seq.ToString());
}
}