Geoff Fudenberg

should `digest`, `parse_region_string` and other functions (in util https://github.com/open2c/cooler/blob/master/cooler/util.py) be deprecated in favor of bioframe versions?

balance_cooler allows store_name even when store=False

1

Should this raise an error? https://github.com/mirnylab/cooler/blob/c9c718fdebccbda41ad10c47f700853f79ee3cd3/cooler/balance.py#L271

add check_integrity utility that can be called at key places, including Cooler instantiation (if indexes are missing, cooler cli currently fails with uninformative errors, as below) cooler coarsen --out test.cool...

square maps

7

would be really nice to be able to easily view a symmetric square region of the genome. thanks!

would it make sense to add this option similar to the one from SRA?

distiller fails silently when out of disk space

1

with command exit status error 141 (pipe error) when calling bwa mem -t 8 -SP {fasta} {R1.fastq.gz} {R2.fastq.gz} | samtools view -bS > {library}.lane1.0.bam | cat when [fputs] No space...

Had a cryptic error when running test_project.yml that was resolved by updating nextflow-- it would be great to document the docker & nextflow versions the code has been tested on.

should there be some available memory checks & warnings issued depending on chunksize etc?

maybe add links in the CLI docstring to this notebook as well?

JASPAR2020_vertebrates error

1

Hello, I am trying to provide the jaspar_2020 database to maelstrom as described: https://gimmemotifs.readthedocs.io/en/stable/overview.html#motif-databases. `gimme maelstrom` seems to run fine I use the default database or provide jaspar 2018 motifs...