Allow N

[killercup]

We were testing with a BAM file where reads have Ns and modkit crashed on the unreachable! in modkit-core/src/pileup/base_mods_adapter.rs:77. I think this "fixes" this by ignoring this position. I also tried to come up with some other places this could be problematic and then also tried to have Claude write tests that exercise this.

[ArtRand]

Hello @killercup,

Out of curiosity, where are you getting sequencing reads with N bases?

Thanks for the contribution, I'll take a look when I start rolling up all the changes for v0.6.2. One thing of note, this code is part of the hottest most critical loop in pileup, so I'll have to make sure there isn't any performance regression. From a quick glance, it should be fine, but I'll need to check. If you have a samply trace from the released version and this one that would save me some time.

[killercup]

Thanks for the quick reply! We're working on https://bitbucket.org/bsblabludwig/rastair which works with TAPS reads and can write modBAM.

Good point about the performance, I can compare this for you. (Might have to wait until tomorrow though)

[ArtRand]

Yes I saw Rastair, looks like a nice project! No rush on the perf data. Thanks for the contribution.