ymcki

samtools 1.15 become very slow when I set maxcnt to 8,000,000

2

I want to use samtools to handle extremely high depth data. So I changed iter->maxcnt = 8000; in sam.c to 8000000. Then it becomes very slow that it becomes not...

### Description I am trying to translate the Reformer machine_translation code https://github.com/google/trax/blob/master/trax/models/reformer/machine_translation.ipynb that was written for trax 1.2.9 to make it work with trax 1.4.1 However, my program crashes when...

How to make sniffles do a better job in splitting insertions at the same location into two het calls?

2

I am running sniffles with HG002 data from ONT on NIST CMRG v1.00 benchmark. This benchmark has 216 SVs. I find that most of the false negatives are due to...

Incorrect SNP representation when it overlaps a deletion

3

When I was trying to run vcfeval with the same vcf generated by Clair3 using the following command, I find that I am getting 3518 out of 5440881 FPs/FNs ./rtg...

Stack overflow seg fault in calculate_clair3_full_alignment

1

I ran a high coverage sample and got seg fault with clair3.py CallVariantsFromCffi running 1.0.4 Running a version of python3.9-debug allowed me to pinpoint the crash at clair3_full_alignment.c:656 which is...

It seems like only insertion, deletion and duplication.

Better documentation about the models?

17

0.5 is released together with [email protected] basecalling model. So we need to think about whether to switch or not. Based on the limited documentation, I only know it is faster...

0.3.x generates reads 10% longer than 0.4.x and 0.5.x???

4

# Issue Report ## Please describe the issue: I am running benchmark to compare performance of 0.3.x, 0.4.x and 0.5.x with both 4.2 and 4.3 sup model. Since 0.3.4 doesn't...

Only one strand of STR basecalled "properly" for a SCA31 case

3

I am using dorado 0.3.2 to basecall my suspected genetic disease cases. One of the cases is confirmed to have SCA31 which can be diagnosed by TGGAA repeat flanked by...

How to improve the reproducibility of dorado across different GPUs?

14

# Issue Report ## Please describe the issue: We used to run dorado on 4xA100 80GB. But my boss asked me to explore running it on 8xT4 16GB. I did...