[Biopython-dev] Alignment object

[Kevin Jacobs <jacobs@bioinformed.com>]

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