Matt Shirley

@simonvh Please note that the pyfaidx bgzip routines are not as efficient as samtools yet. See https://github.com/mdshw5/pyfaidx/issues/126#issuecomment-432654422. I'd love to fully implement bgzip sequence region retrieval in the next pyfaidx...

I've almost completed full implementation of BGZF indexing, and when all test are passing I'll update this thread with a new release of `pyfaidx` that uses the samtools/tabix `.gzi` block...

I've been busy with some other work, but the "correct" bgzf access code is about 90% complete. I'll update here when it's ready.

Hmmm... I haven't paid much attention to the `FastaVariant` class recently. I think indels shouldn't be too hard, but I omitted them originally as I wanted to maintain a 1-1...

Thanks for the feedback. I agree that the bcftools model is appropriate, and if I can get some time, or someone willing to help with the implementation, it will get...

Thanks so much for giving me a reproducible example. I'll have to consider what the expected behavior should be. So far I've been using the [behavior of samtools](http://www.htslib.org/doc/faidx.html#DESCRIPTION) (htslib) as...

I also like the description of indexable FASTA files in the [samtools documentation](http://www.htslib.org/doc/faidx.html#FASTA_Files), but it says nothing about empty lines: >In order to be indexed with samtools faidx, a FASTA...

Hey @archanaraja thanks for raising this issue and apologies for the late response. I'm not familiar with the Google Cloud Storage apis and was not planning to implement this. If...

This looks like a good idea (thanks for sharing the PEP). I’d love some help on this as I’ve not used this system before.

Thanks for sharing this tool. I do currently tag releases, and use semantic versioning to build version numbers for test packages. The CI releases package builds to test-pypi and pypi...