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I've been building 'genome-wide' prgs for gramtools by building one prg per msa/locus, and then adding in the linear reference genome seq in between.
I'd like an option for make_prg to do that. I c…
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# 🌟 FAVOR+ / Performer attention addition
Are there any plans to add this new attention approximation block to Transformers library?
## Model description
The new attention mechanism with linear…
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This is the sibling lineage of LF.3.1.1 previously described as Branch 2 in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1558.
It is still a small lineage but having been sampled i…
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**Are you using the latest release?**
`funannotate v1.8.11`.
**Describe the bug**
funannotate test is failing at the predict step with error "Not enough gene models 175 to train Augustus (200 re…
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### **Description** Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1594
**Sub-lineage of:** KP.2.3 (= JN.1 + S:∆S31, S:H146Q, S:R346T, F456L, V1104L + ORF3a:K67N + O…
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Current Bubble Tea input handling is quite limiting as it doesn't support parsing input events such as cursor position report, fixterms & Kitty keyboard, and other terminal features. This is because w…
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I'd like to extract reads from a .gam file that do not align to any nodes that are in a reference path. My end goal is to identify coverage and depth of likely insertions.
Commands that strike me a…
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Hey guys,
I have a few questions from my run with the updated evSeq scripts:
1. Is there an uninstall script for the local version, in particular for the GUI? Could be worth adding info to docs.…
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I am currently attempting to `merge/collapse` VCFs produced by DELLY, LUMPY and MANTA using Truvari. Two of the VCFs produced are in the 4.2 specification and one is produced in the 4.1 specification.…
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Hi all,
I understand SAM output is not optimized and it is discouraged, however I had to test it and I run into some issues.
First of all, output is uncompressed and I couldn't pipe into samtools …