snajder-r

Fixed error when PATH is not set

3

Default for a missing `PATH` should be an empty string, not an empty list. Otherwise trying to call `.split` on it will throw `AttributeError: 'list' object has no attribute 'split'`

Modified base calling: Skipped bases in bam MM tag

1

Hi! The current SAM specification of the MM tag says: > Following the base modification codes is an optional ‘.’ or ‘?’ describing how skipped seq bases of the stated...

Initialization error (related to koi)?

5

Hi! We're trying to run bonito basecaller and are experiencing some issues. $ bonito basecaller --reference reference.mmi --device cuda:0 -- [email protected] reads_directory > loading model [email protected] > loading reference >...

Unable to train joint model from pretrained cpg and dna model with tensorflow backend

1

Hi, I was able to train the joint model successfully. Then I wanted to train the cpg and dna model separately and the joint model on top. Training cpg and...

GPU utility in training only about 25%

1

Hi! When trying to train DeepCpG, on a GPU system, I get very low GPU utility (approximately 25%). Do you perhaps have an idea what could be the cause? I...

perf: Average NamedList __getitem__ performance improvement

1

### Description Previous NamedList performance is optimized for integer/slice (list) access, but very slow when using string indices. With this change, both types of access are approximately equally fast and...

Make parameters visible to input and output

12

The **params** allow us define arbitrary parameters that can be referenced by **shell** and **run**. The **input** and **output**, however, cannot refer to the parameters (and vice versa). Sometimes it...

Hi, I installed VDJVIZ on Ubuntu. I'm logging in with the default user, and then I'm trying to upload new samples. When I do so, I get an error "Error...

This is probably low-priority, but it seems like a bug. I was trying to put a line break into a class name as a workaround for #1081, annotating the class...