[Biopython-dev] CFFI bindings for sambamba

[Artem Tarasov]

Hello BioPython,

As you may know, during the previous GSoC I wrote a library for working
with SAM/BAM in D. Only recently the language gained shared library support
on Linux. And at about the same time PyPy 2.0 was released.

I had some spare time last few days and made bindings for the library. At
the time they are a bit incomplete and lack tests and documentation. They
work on Linux with PyPy 2.0 or CPython 2.*.

On PyPy, the performance is not worse than that of PySam on CPython, thanks
to the powerful JIT.

Features so far:
* BAM reader and writer, both can use multiple threads for (de-)compression
* Random access, creating BAI index
* Fast pileup engine (optionally uses MD tags to determine reference bases)

The repository is at https://github.com/lomereiter/sambamba-bindings
Again, currently only Linux is supported. Bug-hunting and pull requests
with tests and docs are much appreciated.



--
Artem