hts.cr VS htslib

First, let's make sure that Samtools can be built successfully. Note that the build requires htslib and other dependencies. In my case, I put htslib directory in the same directory as samtools because I build htslib by myself for htslib binding of Crystal language which I make for my personal interest. If you put htslib here, samtools can detect it automatically. htslib requires submodules git submodule update -i --recursive. If you get stuck, please google it. It would be safer to check out a stable tag git checkout 1.16.1, and switch to a new branch git switch tanuki. It is up to you.

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

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:

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

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.

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.