Anton Goloborodko

storing bgzip-compressed genomes

12

hi! Many thanks for writing this amazing library!! One issue that personally prevents my lab from switching to genomepy is that it seems to store genomes in uncompressed .fa files....

store the CLI command that was used to create a cooler?..

2

if a cooler was created via the CLI, we could store the exact command + arguments that were used to create it, like pairsamtools already do it. It's very useful...

https://github.com/mirnylab/cooler/blob/e40447d1e127db4a846c4dc63bf1823716f27313/cooler/api.py#L536 given that the bins table is naturally indexed by bin_ids, why not use the faster fancy indexing instead?

in cload pairs, use DCIC pairs format by default

1

Currently, cooler cload pairs requires specifying which columns contain chrom1, chrom2, pos1, and pos2. Yet, the field already has a well-established standard, the DCIC pairs. It would make a lot...

a thread to discuss the new experimental pipeline. My couple of minor suggestions: 1) why use the name "pipe" if "apply" if there is the more standard name "apply"? Also,...

https://github.com/mirnylab/cooler/blob/e40447d1e127db4a846c4dc63bf1823716f27313/cooler/tools.py#L262

metadata for cooler balance is hard to find

7

currently, the parameters of balancing are stored as a metadata of a particular column of the bins table, which is really hard to find. While this is technically valid, on...

showing all SRRs for a particular GSM

1

Hi! Thanks for this awesome project, a much-needed tool in the Python ecosystem. I wonder if you could consider addiing a separate data structure to each GSM object that would...

add phasing using pairtools phase. Add a built bwa-latest to the container.

discovered by Joaquim Olle: People who start working with distiller would run the test first, then modify the .yml file for their project and run it again. If the ./results...