Matt Stone

Probably. 🙂 And update the validation to enforce that there may be only one fastq for the specified sample and read number per lane (e.g. a sample can't have two...

Thanks @tfenne. The `util` module already exists, and includes the `inspect`, `logging`, `metric`, `string`, and `types` submodules. I think refactoring the package to remove the existing `util` module falls outside...

`vendor` is typically reserved for vendored copies of third-party packages. e.g. in `vendor/illumina/` I might expect to find a (possibly patched) copy of [BeadArrayFiles](https://github.com/Illumina/BeadArrayFiles). Could the two of you please...

Works for me!

I reworded this issue to more narrowly scope it to the tests reorganization (thanks @nh13 for doing this in #135 ), and opened #136 to address the remaining reorganization

I'm also surprised that the number of pileups changes when duplicate reads are excluded - given that pileups are reported with any number of supporting reads, I would expect the...

+1 for making `Template` iterable over the constituent alignments. I would suggest defining each iterator as a `property` instead of a method. (I find it more pythonic, though that may...

I'm cautious that the proposed behavior could lead to some unexpected footguns. Specifically, having `r(1|2)_supplementals` and `r(1|2)_secondaries` not return all alignments with the corresponding flag might be surprising to users....

I have never seen pysam create an `AlignedSegment` with the string literal `"*"` in either the `query_sequence` or `query_qualities` attribute. Additionally, the `query_qualities` attribute is typed as `array | None`,...

Here's the code in question. ### Query sequence https://github.com/pysam-developers/pysam/blob/0eae5be21ac3ab3ac7aa770a3931e2977e37b909/pysam/libcalignedsegment.pyx#L544-L545 If the [length of the query sequence on the corresponding struct](https://github.com/pysam-developers/pysam/blob/0eae5be21ac3ab3ac7aa770a3931e2977e37b909/htslib/htslib/sam.h#L209C1-L209C53) is zero, `query_sequence` is set to `None` ### Query qualities...