protected AlignmentPairFilter(bool removeFailedPairs = true, ReadPairEvaluator pairEvaluator = null)
{
_removeFailedPairs = removeFailedPairs;
OnLog = Console.WriteLine;
_readsWaitingForMate = new Dictionary <string, ReadPair>();
_pairEvaluator = pairEvaluator ?? new ReadPairEvaluator();
}
/// <summary>
/// Constructs an AlignmentPairFilter.
/// </summary>
/// <param name="removeFailedPairs">Whether to remove ReadPairs once they have returned "true" from ShouldSkipPair. Default = true. If false, allows the pair to continue collecting reads and be re-evaluated.</param>
/// <param name="pairEvaluator">Read pair evaluator for custom behavior.</param>
/// <param name="requireSupplementaries">Whether the read pair requires all expected supplementary reads to be present in order to be considered complete. Default = true.</param>
protected AlignmentPairFilter(bool removeFailedPairs = true, ReadPairEvaluator pairEvaluator = null,
bool requireSupplementaries = true)
{
_removeFailedPairs = removeFailedPairs;
_requireSupplementaries = requireSupplementaries;
_readsWaitingForMate = new Dictionary <string, ReadPair>();
_pairEvaluator = pairEvaluator ?? new ReadPairEvaluator();
}
