Clint Valentine

It is possible to run the tool `CollectDuplexSeqmetrics` on a consensus BAM file but the results will not be intuitively correct since metrics collection is expecting the input be **_raw...

@nh13 @tfenne would you be willing to approve this PR or identify alternative code owners for auto-review assignment? After this PR is merged, the repository settings will be updated to...

Consider more advanced views into the alignments in Template

4

After fixing an issue in `Template` where records were added twice to different internal fields in this PR: - https://github.com/fulcrumgenomics/fgpyo/pull/203 We might want to consider more specific "views" into the...

Add AuxAlignment for parsing secondary/supplementary alignments in SAM tags

2

Prior drafts are [here](https://github.com/fulcrumgenomics/fgpyo/pull/208) and [here](https://github.com/fulcrumgenomics/fgpyo/pull/206). - [x] Add a few more unit tests to get back up to 100% coverage

Closes: https://github.com/fulcrumgenomics/fgsv/issues/41

### Description I'd like to encode `None` as the string `"."` and decode it back to None. All other behavior of this library is extremely desirable and functional, but I...

### Description of feature I am experimenting with custom CSS to alter the look and feel of MultiQC reports but one thing I have not figured out yet is how...

Often ignore hard clipping when fetching unclipped ends

5

Closes https://github.com/fulcrumgenomics/fgbio/issues/1030 Most code that needs to find the reference location for the aligned bases of reads plus clipping operators has defaulted to consider both soft and hard clipping operators....

Use a Git cliff TOML for releases

2

I noticed a typo in the release action; we don't have a `pyproject.toml` to read from.

The test fixture used to create a single-interval `IntervalList`, despite allowing parameterization, always returns an interval in the range `[1, 10]`. Fixing this bug causes many unit tests to fail....