Enrico Seiler

> Hi, > > When I run this with --illumina-read-length 300, it works. But with 500, it has a `Segmentation fault (core dumped)` issue. > > I have tried `ulimit...

There's a note: ```             // NOTE: We can only insert CGAT, but we can have a polymorphism to N. ``` But the code seems weird anyway. Why not randomly sample...

Resolved by #3259

Hey there! ### Version The version you are using has some major refactorings. That's also why the `Timings` show `0.00` seconds for most of the statistics. The results should be...

I have the same problem, for now you can just add (as a workaround) ```yaml - run: ln -s /opt/conda/bin/git /bin/git ``` to your `bioconda-recipes/.circleci/config.yaml` between lines 80 and 81:...

As far as I understand, this should now work? ```cpp auto config = seqan3::align_cfg::method_global{} | seqan3::align_cfg::scoring_scheme{seqan3::hamming_scoring_scheme{}} | seqan3::align_cfg::min_score{-10}; seqan3::align_pairwise(std::tie(reference, query), config); ```

> I tried following the example in the docs and the speed didn't improve for me. Looks like you forgot to reference the example you tried out?

Here are some reduced examples and possible fixes: ### Assertion failed : data_begin_position 2R CTCAAGATACCTTCTACAGATTATTTAAAGCTAGTGCACAACAACAATAAATTGACTAAG TTATGTCATTTTAAGCGGTCAAAATGGGTGATTTTTCGATTTCAAGTACCAGGCGAACAG AAGACACCTTCTAGAGATTCTGTTCAACTGGTAAGCAAAAACAGTAAATTGCCTAAGTTT AACAATTTAAGCGGTCAAAATGGGTGATTTTCCGATTTCAAGTACCAGACAAACAGAAGA TACCTTATACAGATTATTTAAACCTGGTACACAAAAACAATAAATTGACTAAGTTATGTC ATTTTAAGCGGTCAAAATGGGTGAATTTCCGATTTCAAGTAATAGGCGAACTCAAGATAC CTTCTACAGATTATTTAAAGCTAGTGCACAACAACAATAAATTGACTAAGTTATGTCATT TTAAGCGGTCAAAATGGGTGATTTTTCGATTTCAAGTACCAGGCGAACAGAAGACACCTT CTAGAGATTCTGTTCAACTGGTAAGCAAAAACAGTAAATTGCCTAAGTTTAACAATTTAA GCGGTCAAAATGGGTGATTTTCCGATTTCAAGTACCAGACAAACAGAAGATACCTTCTAC AGATAATTTAAACCTGGTACACAAAAACAATAAATTGACTAAGTAATGTCATTTTAAGCG GTCAAATTTGTGATTTTTCGATTTCAAGTACCAGGCGAACAGAAGACACCTTCTAGAGAT TCTGTTCAACTGGTAAGCAAAAACAGTAAATTGCCTAAGTTTTACATTTTAAGCGGTCAA AATGGGTGATTTTCCAAATTAAAGTACCAGACAAACAGAAAATACCTTCTAGATATTCTG TTCAACTGGTAAGCAAAAACAGTAAATTGCCTGAGTTTTACATTTTAAGCGGTCAAAATG GGTGATTTTCCGATTTCAAGTACCAGACAAACAGAAGATACCTTCTACAGATTATTAAAC...

> Also, I noticed that the VCF produced by `mason_variator` is not sorted. You are right, and VCF requires POS to be sorted. The problem is this code (for the...

> Unfortunately, the crashes still exist. And even more annoying is that they occur only on the 7 Gbp rye genome, so each round of varying the parameters takes ages...