search

seqan / seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
https://www.seqan.de
Other
407 stars 82 forks source link

[IO] VCF/BCF support #2953

Open cauliyang opened 2 years ago

cauliyang commented 2 years ago

Question

Hi dev-team!

I really like the library and learning how to use it. However, I am curious about what is the progress to implement annotation_file input/output for (vcf/bcf/..). I notice that https://github.com/seqan/seqan3/projects/23#card-28054215 . Is there a plan to release this module recently? 🤔

Thanks for your reply!

smehringer commented 2 years ago

Hi @cauliyang ,

thank you, that is great to hear!

We are currently debating whether we will wrap or adapt to the https://github.com/h-2/b.i.o. library that is developed by one of our senior developers who left us after finishing is PhD. We are working closely with him but no decision has been made.

The B.I.O. library currently has support for vcf/bcf in and output as far as I know, as well as FASTA/Q reading. SAM/BAM is in the process .

If you have the use case and the time to try the vcf/bcf parser of B.I.O., it would be very helpful for us if you'd give us feedback! It could influence the decision if we adopt the B.I.O. API in seqan3.

I don't have a specific time frame right now when the I/O module will be tackled but it is on our list soon.

Best, Svenja

cauliyang commented 2 years ago

Hi @smehringer,

Many thanks for your kind reply 😄 , and I also notice B.I.O. I know maintaining a repo is not easy, and I really respect your work. I am also reading the books "sequence analysis and modern c++" from Hannes. It is great!

I will try to use the B.I.O library in my project. I hope this project goes well and becomes the golden standard in sequencing analysis 🚀 .