Armin Töpfer

Food for thought, I've added `data/clr1.txt` that contains one pair of two full-length subreads ``` $ ./at ../data/clr1.txt | 20220420 19:05:25.732 | INFO | Number of sequence pairs : 1...

If I unfold the macros, I get to this line, but not sure if it's the correct line: https://github.com/lh3/minimap2/blob/ace990c381c647d6cf8fae7a4941a7b56fb67ae7/krmq.h#L354

I would appreciate if the code passes sanitizers. Thank you

>I definitely believe such a feature is publishable on its own NGMLR published it and minimap2 uses a two step approach.

[cram](https://bitheap.org/cram/) is the best tool for this.

In my opinion, we can rather provide samtools one-liners to extract certain information in a different format.

Thank you for hint. It's unfortunate that `snakemake` broke this....please use an older version until we get to fixing this.

We are in the process of deprecating IPA. Please use alternative HiFi genome assemblers, such as https://github.com/chhylp123/hifiasm

Can you provide a small reproducible example that you can share?

Does `lima` v2.9.0 from bioconda / [github](https://github.com/PacificBiosciences/barcoding/releases/tag/v2.9.0) work?