Chris Wright

VCF Draft 4.5 and Modified Bases

29

Following [x.com/@fiamh](https://x.com/fiamh/status/1782261875876692322) I was made aware of the proposal for how to store modified base information in VCF files. A quick search and I could not find any public discussions...

* Add a thread pool to speed up bam decompression during index build. I've tested that the index is unaffected by this; though I don't understand htslib enough to know...

Clarification on `reads` argument

2

The README states multiple BAM files can be provided to `bambu()`. Reading the entire documentation suggests the intention here is that each BAM corresponds to a separate sample to be...

arm64 linux builds

2

I'm assuming the list of build platforms is supposed to contain the arm targets rather than duplicate x86 ones? I've come back to this because some of my own CI...

Pymake

3

This PR redoes https://github.com/lh3/minimap2/pull/868 only it adds the crucial `include *.c` into the MANIFEST file used to create the source distribution tarball. It can be tested with: ``` python setup.py...

Passing a quoted string starting with `-` to nextflow CLI has unexpected behaviour

1

## Bug report ### Expected behavior and actual behavior I would anticipate that passing arguments such as `--minimap2_args '-k15'` would result in the parameter `minimap2_args` being set to the string...

I've filed this as a bug only because my understanding of what it appears to me that the intent was, but maybe its a feature request. #### Are you using...