Pileup API

[Andrew]

I am wrapping parts of the bamtools API for Python access. I am
wondering whether it is safe to work against the pileup API, as I
notice the code is not under the api folder. Is the public interface
to pileup code relatively stable?

Thanks,
Andrew

[Derek]

I'm already planning to pull the PileupEngine/Visitor code out of the
auxiliary utils lib and drop it into the 'official' API sometime in
the near future (likely into a BamAlgorithms::Pileup). The code
itself is relatively stable, so I'd say you're probably safe to wrap
those features for your own use.

But since those classes & methods WILL be moving to a completely
different library (and some naming may change a bit), I'd advise not
distributing your wrapper too widely until then. Or at least that part
of it.

Hopefully that makes sense.
- Derek

[Andrew]

Thanks for the quick reply.

That sound perfect. I assume this means that the pileup code will end
up in the include/ directory after compiling as well. That would be
ideal as I could avoid packaging the header files with my code, and
instead point to that folder.

Thanks again,
Andrew

[Derek]

You're spot on - that's the plan.
- Derek

[andrew.m...@gmail.com]

Any update on when the pileup code will be added to the api?  Also, Andrew, is your code public?  Thinking of wrapping bamtools for python also, but wouldnt want to replicate anyone elses good work.

Thanks,

Another Andrew

[Derek]

Andrew(s) and anyone interested,

Sorry this has stagnated (at least from an update standpoint) for so long. 

Full status update:

I've currently got a BamTools 3.0 version in the works that exposes the Pileup API to the main library, along with other improvements (most notably cleaning up the build/install process). While I'm primarily focused on other projects at the moment, the main application that I'm working on is using the 'experimental' BT3 under the hood - so it's getting polished it and stress-tested as we go. Once I feel comfortable enough with it, I will add a new 'release candidate' branch to the github repo. At that point, users may choose to either try out this v3-rc branch (and hopefully provide feedback), or continue to use v2.x from the master branch. After some time in the wild, I'll make a official version update on the master branch to the new v3.0 - with updated docs, porting guide, etc.

I don't have an exact timeframe set, but it shouldn't be too much longer, at least for the release candidate branch. Thanks for your patience.

Thanks for all of your feedback & suggestions.

  - Derek

[Ben Ainscough]

Are there any updates on a BamTools version 3.0. I could really use this pileup in the API.

Thanks,

Ben