James Bonfield
James Bonfield
> Good progress has been made on this. Both [read](https://github.com/zaeleus/noodles/blob/91bc4bd83cd9f2f04ce45ba65982996bd5ac1189/noodles-util/examples/util_alignment_view.rs) and [read/write](https://github.com/zaeleus/noodles/blob/91bc4bd83cd9f2f04ce45ba65982996bd5ac1189/noodles-util/examples/util_alignment_rewrite.rs) examples can be viewed and tested. > > ```shell > # SAM/BAM/CRAM => SAM. The output is written...
I appreciate this isn't easy to study, so if you wish to see what the differences are between the functions, then here is what it looks like with ksw_global replaced...
When we submitted our [Samtools-update](https://academic.oup.com/gigascience/article/10/2/giab008/6137722), Bcftools and Htslib papers last year to GigaScience it was a hard requirement that we also submit the RRID numbers. It turned out these already...
I think the real issue is how to easily generate documents that can be cited in the traditional ways. I agree RRID may not be appropriate for documentation. Publishing in...
At the meeting we discussed how to proceed from here. I'll tidy this up and make sure it's rebased and update any history comments (which will be way out of...
This doesn't seem like the sort of thing we'd want to implement, as it's questionable as to whether this is the correct approach and there are lots of corner cases....
As long as you've done appropriate filtering and every read occurs exactly once across all of your files, then it should work provided all the files have the same sort...
Mixture of ideas from our samtools meeting (and some others). * With deep data, a considerable bottleneck is fetching the seq and/or qual and they can fall out of the...
Unfortunately we've got 2 new projects on the go in addition to samtools (and the team hasn't been given any more resources) so our resources are stretched. So we can't...
As the debate has been opened, my twopennies worth. My heart sinks whenever I'm attempting to install something that has a dependency on vast C++ libraries. I don't know anything...