tnnandi

conda import environment not working

1

When I try creating a conda env from the provided yml file, I get an error report that ends with the following: File "C:\Users\tnnan\anaconda3\lib\site-packages\ruamel_yaml\scanner.py", line 651, in fetch_value raise ScannerError(...

Number of sequences in BAM header mismatches reference

5

Hi, When I am using SvABA with the hg38 (no alt) reference file and a BAM file obtained by aligning a whole human genome to the same reference, I get...

Installation issue

10

Hi, When I'm trying to install SvABA, ./configure works fine but make gives the following error: ``` gcc -g -Wall -O2 -Wno-unused-function libfml.a example.o -o fml-asm -L. -lfml -lm -lz...

ValueError: Argument is not writable

3

### Operating system Ubuntu ### Platform 64 bit x86 ### OpenSlide Python version 1.3.1 ### OpenSlide version 4.0.0 ### Slide format SVS ### Issue details Hi, When I try to...

AttributeError: 'pysam.libcalignmentfile.AlignmentFile' object has no attribute 'get_index_statistics'

1

Hi, I'm using the following version of pysam and getting the error: `ref_info = aln_file.get_index_statistics(), AttributeError: 'pysam.libcalignmentfile.AlignmentFile' object has no attribute 'get_index_statistics'` when I execute `./SVision -o svision_out/ -b ./supports/HG00733.svision.demo.bam...

[CLI]: wandb doesn't report logs from all nodes for distributed training using HuggingFace trainer

2

### Describe the bug By default, simply adding "report_to": "wandb" as an argument for training_args (for HF Trainer) only creates plots (say, for GPU usage) for only the master node...

Generating reads with even 10X coverage for WGS is taking too long

1

Hi, I'm trying to generate reads with 10X coverage for a genome with a size of 3 billion bp and a read length of 2x150 bp. This leads to a...

Weights & Biases doesn't report logs from all nodes for distributed training using HuggingFace trainer

18

### System Info torch 2.1.2+cu118, transformers 4.39.3, accelerate 0.29.1, deepspeed 0.14.0, wandb 0.16.6, python 3.9.0 ### Who can help? @pacman100 @muellerzr ### Information - [ ] The official example scripts...

SV calling using giraffe/vg

1

It's not very clear to me how exactly VG or Giraffe carries out SV calling (if it truly does). The tutorials mention how we can do genotyping using existing SV...

[BUG] Issue with multi-threading when using blur filtering

1

## Description ## To Reproduce Steps to reproduce the behavior: 1. Choose 'blur' for qc in the tile extraction step: ``` dataset.extract_tiles(qc='blur', # ‘otsu’, ‘blur’, ‘both’, or None # qc.GaussianV2()...