Nils Homer

No worries, you're not being a jerk, and same here. Tone is super difficult in written text. @tfenne was the original author of MergeBamAlignment, and I helped maintain it for...

> be a) queryname sorted or grouped (i.e. all records with the same name are grouped together in the file) The latter (grouped) means that the "all records with the...

@johanneskoester all tests pass; I think this is ready for review

@johanneskoester done, waiting for tests to pass

That's a tough one at first blush, since if we have a mate that's on a different chromosome, we'd have to retrieve it as well, and depending on the output...

I could see writing a class that implements a `SamWriter` that takes (1) a writer to write the final records to, (2) a reader with _all_ reads. When you write...

An example would be #1037, but I'd want to flesh it out and wire it in.

I haven't tried it, but if you stuck in some dummy values into the `RX` tag before grouping (`RX:Z:A` for single UMI and `RX:Z:A-A` for duplex), you could then run...

See `/A` and `/B` https://github.com/fulcrumgenomics/fgbio/wiki/Developer-Note:-Tracking-Reads-through-Grouping-and-Duplex-Consensus-Calling Forward strand of the genome? Or forward strand of the original source molecule? It's an overloaded term for duplex sequencing...

Validates locally if I use: ```console bioconda-utils lint --loglevel debug --full-report recipes/fqgrep ``` but not the following (when [`6144f7b3397dac92a72036fe4981add6a50c6bef`](https://github.com/bioconda/bioconda-recipes/commit/6144f7b3397dac92a72036fe4981add6a50c6bef) is checked out) ```console bioconda-utils lint --loglevel debug --full-report --git-range origin/master...