Yara Index Memory alignment issue

[svnbgnk]

Due to copying a dna5 alphabet into a dna4 index the resulting indexing data structures are no longer completely correct. This will affect the mapping process (backtracking) in extremly rare cases.
https://github.com/seqan/seqan/blob/f5f658343c366c9c3d44ba358ffc9317e78a09ed/apps/yara/indexer.cpp#L255-258.

I fixed this issue on a branch in Dream-Yara here:
svnbgnk/dream_yara@a02684a
I will submit a PR for Yara soon.

[rrahn]

So the silent conversion of 'N' to 'A' when converting dna5 to dna4 will cause this issue?
In general, would mapmap be a complete replacement of Yara? If so, then I would continue to apply this fix to SeqAn and focus on mapmap being ported to SeqAn3. Otherwise, if we are porting yara to SeqAn3 we can also make the fix there (if relevant).