Matt Stone

Support for S3 hosted BAM files?

3

Hi, Is it possible to access S3 hosted BAM files with `seqan::BamFileIn`? Htslib permits it but I couldn't find any documentation describing it here. Thanks!

SetMateInformation should add the MQ tag to any supplementary alignments

1

Currently, `SetMateInformation` does not add the `MQ` tag to supplementary alignments. I'm not sure if this is intended behavior - the docs suggest that supplementary alignments would have this tag...

feat: add --umi-prefix to CopyUmiFromReadName

1

https://github.com/fulcrumgenomics/fgbio/issues/957

## Problem Some UMIs produced by BCL convert are prefixed with "r", indicating "reverse complement."[^1] > When sequencing a run with Unique Molecular Identifier (UMI) situated in the index2 (i5)...

CIGAR operations out of range after splice junction correction

5

Hi, Since the update in #14 to update transcripts after correcting splice junctions, I get the following error. I think there may be a bug in the `rescueNoncanonicalJunction` function, which...

Show total count of child checkboxes in cookie?

3

Hi, Does vim-orgmode support the `org-checkbox-hierarchical-statistics` setting, or an equivalent? http://orgmode.org/manual/Checkboxes.html Thanks!

The Workflow class cannot be imported due to a circular import

1

**Snakemake version** 8.10.0 (The latest available via conda. As far as I can tell this has not been patched since.) **Describe the bug** Importing `Workflow` produces an `ImportError` due to...

`io.assert_path_is_writeable()` should return True for "/dev/stdout"

1

```py In [5]: io.assert_path_is_writeable(Path("/dev/stdout")) --------------------------------------------------------------------------- AssertionError Traceback (most recent call last) Cell In[5], line 1 ----> 1 io.assert_path_is_writeable(Path("/dev/stdout")) File ~/.mambaforge-x86/envs/gta/lib/python3.10/site-packages/fgpyo/io/__init__.py:108, in assert_path_is_writeable(path, parent_must_exist) 106 # If file exists, it must...

this can be typed more specifically than `Any`

feat: Add asdict()

4

I'd like to add a function to convert a `Metric` instance to a dict. (In support of #107 ) I'm currently receiving the following mypy errors, which I suspect are...