[Biopython-dev] Alignment object

[Aaron Quinlan]

Hi Kevin,
  Per the author, BamTools supposedly now supports all endian flavors.
Aaron

On Mar 4, 2010, at 9:07 AM, Kevin Jacobs wrote:

> On Thu, Mar 4, 2010 at 8:52 AM, Kevin Jacobs <jacobs at bioinformed.com> <bioinformed at gmail.com> wrote:
> On Thu, Mar 4, 2010 at 8:33 AM, Aaron Quinlan <aaronquinlan at gmail.com> wrote:
> Just an FYI for those interested in developing tools to work with BAM: it may also be worth looking into the BamTools C++ API developed by Derek Barnett at Boston College (http://sourceforge.net/projects/bamtools/).  The API is quite nice and has much of the necessary functionality for iterators, getters/setters, etc.
> 
> I added BAM support for my BEDTools package (http://code.google.com/p/bedtools/) using the BAMTools libraries.  Save for a few minor bugs along the way, it was rather straightforward to include.
> 
> Thanks for the tip, Aaron.  I was unaware of both bamtools and bedtools.  The bamtools code looks well designed and quite similar to my emerging Cython/Python rendition.
> 
> 
> Ouch-- never mind.  The bamtools code isn't endian-clean -- it will only work correctly on native little-endian architectures.
> 
> -Kevin
>