Nils Homer

@tfenne I would agree that it looks to me like it should be secondary and not supplementary based on the terminologies defined in the SAM spec. That said, I usually...

We use the [`SetMateInfoIterator` from htsjdk](https://github.com/samtools/htsjdk/blob/b16416c078e2df3e3a21486207d0c0c31b293cb9/src/main/java/htsjdk/samtools/SamPairUtil.java#L416) which routes to the [`setMateInformationOnSupplementalAlignment` method](https://github.com/samtools/htsjdk/blob/b16416c078e2df3e3a21486207d0c0c31b293cb9/src/main/java/htsjdk/samtools/SamPairUtil.java#L308C24-L308C65) It looks like MQ is not set on the supplementary records, so we'd likely need to make a...

- [x] PR into HTSJDK: https://github.com/samtools/htsjdk/pull/1737 - [x] HTSJDK released with PR above (see https://github.com/samtools/htsjdk/releases/tag/4.2.0) - [ ] This PR updated with new HTSJDK

Whatever we do here, we probably want to do for: - https://github.com/fulcrumgenomics/prymer/pull/127 - https://github.com/fulcrumgenomics/pybwa/pull/59 - https://github.com/fulcrumgenomics/python-template and others. My motivation was to include PR links and attributions, which the `--config...

@kabilov that's a really good suggestion. For our future self, [here](https://github.com/fulcrumgenomics/fqtk/blob/f74eb6c4939c2db123067e50c7e76c07777ebdc2/src/bin/commands/demux.rs#L718) is where a different output types could be specified in the code

I would welcome an internal discussion with stakeholders to see if this is something we want to do.

Fixed in https://github.com/fulcrumgenomics/fgpyo/pull/256

The `CallDuplexConsensusReads` tools use the `Consensus` agreement and disagreement strategies. We do not expose both as command line options to the tool, like we do for `CallOverlappingConsensusBases `. Running both...

@mashehu thank-you for the review, I've added a test and improved a few others while I'm there.

@mashehu that makes sense, but is difficult in the current state of implementation where we have a list of component names to filter against, not directories. An alternative would be...