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There are some 'N' and other extended nucleotides in the germline sequences.
As we store in the indexes both the k-mers and their reverse complement, and as
we handle extended nucleotides almost randomly (see tools:nuc_to_int()),
we may have slight differences when analyzing some reads and their reverse complement.
Ignoring such k-mers allow thus to be more deterministic, getting the same
results on a (pure ACGT) read and its reverse complement.

Another option (harder to implement) could be to add several k-mers in the index,
but this would decrease the effective weight of the seed.

Note that we should also improve the analysis of reads that includes extended nucleotides.