| htslib | ffi | |
|---|---|---|
| 7 | 5 | |
| 775 | 2,059 | |
| 1.5% | 0.5% | |
| 8.9 | 8.9 | |
| 5 days ago | 12 days ago | |
| C | Ruby | |
| GNU General Public License v3.0 or later | BSD 3-clause "New" or "Revised" License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
htslib
- Gentoo -Os vs -O3 application startup time?
- Does anyone know of a repository for actual genetic data?
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Pigz: A parallel implementation of gzip for multi-core machines
There is another nice multi-core gzip based library called BGZF[1]. It is commonly used in bioinformatics. BGZF has the added advantage that it is block compressed with built in indexing method to permit seeking in compressed files.
[1] https://github.com/samtools/htslib
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Tips for scalable workflows on AWS
In contrast, processing can start immediately and only transfer what is necessary if tooling can read bytes of data directly from Amazon S3. Tools based on htslib can do this, so you can run something like:
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Software Development Project
Another idea is add in reading cloud data natively e.g. htslib which samtools relies on can read s3 directly. https://github.com/samtools/htslib
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Interested in Bioinformatics / C pair-programming opportunity / learning / portfolio project.
Greetings! I'm a bioinformatics software dev in San Francisco and I'm looking for others interested in working on a high-performance genetic data analysis project. The project is in C, using https://github.com/samtools/htslib.
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ffi-bitfield
I'm working on a bioinformatics-related binding called ruby-htslib. htslib makes heavy use of bit fields throughout the library, so supporting bit fields is inevitable.
ffi
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Mixing FFI, Fiddle, and C Extension in Ruby
If you're working with Ruby and need to invoke a function written in C language, there are some convenient gems available: Ruby-FFI and Fiddle.
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Desperately need help with react-native init and ruby
Could this be related to spaces in the directory/this issue: https://github.com/ffi/ffi/issues/623? If so, there's no suggestion on the issue, but https://stackoverflow.com/a/64083281 (including the comment https://stackoverflow.com/questions/62368342/rails-bundle-cant-install-gem-ffi#comment123868330_64083281), might help.
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Why Authorization Is Hard
Hey, Oso engineer here. Good question.
The rust core is indeed called from the ruby library (as it is with all of our 5 other host libraries). The core itself is pretty complex (there's a whole parser/interpreter in there), so maintaining it in a bunch of languages would be a bit hectic.
There are some files inside `lib/oso/polar/ffi` that define the C bindings used by the rest of the library. Here's an example: https://github.com/osohq/oso/blob/main/languages/ruby/lib/os...
We use the ffi gem to make that work: https://github.com/ffi/ffi
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ffi-bitfield
Ruby-FFI is a powerful tool to create bindings for C language libraries in Ruby.
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Travis CLI installation issue for MacOS
Tried solution mentioned here https://github.com/ffi/ffi/issues/653 but no luck then I posted this question over StackOverflow :
What are some alternatives?
genozip - A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
cerbos - Cerbos is the open core, language-agnostic, scalable authorization solution that makes user permissions and authorization simple to implement and manage by writing context-aware access control policies for your application resources.
seqtk - Toolkit for processing sequences in FASTA/Q formats
dd-trace-rb - Datadog Tracing Ruby Client
bwa-mem2 - The next version of bwa-mem
angular-upload-s3cf - This include angular build creation, upload to S3 and clearing CloudFront cache.
cyvcf2 - cython + htslib == fast VCF and BCF processing
OPA (Open Policy Agent) - Open Policy Agent (OPA) is an open source, general-purpose policy engine.
aws-genomics-workflows - Genomics Workflows on AWS
oso - Oso is a batteries-included framework for building authorization in your application.
libdna - ♥ Essential Functions for DNA Manipulation
Ory Keto - Open Source (Go) implementation of "Zanzibar: Google's Consistent, Global Authorization System". Ships gRPC, REST APIs, newSQL, and an easy and granular permission language. Supports ACL, RBAC, and other access models.