[Biojava-dev] Extended ABIF Parser and SCF Writer

[Micha Sammeth]

Hi,

the time I worked on SCF and ABI files is a bit ago, but lets see if I 
can contribute something here. Working since a year on NGS, I could 
imagine that readers for the standard-output of pipelines by Illumina & 
Co would also fit there.

If there is a reader module, I would plead for a low-level interface for
accessing sequences/qualities and re-usable data containers during I/O. 
But maybe that is rather an early stage to talk about that when not even 
the existence of the module is decided.

cheers - micha.

Andreas Prlic wrote:
> Hi Franklin,
> 
> The theme of the moment is modularization... I wonder if we should make a
> module for parsing the output of sequencers...
> 
> This topic is also a bit related to the discussion we had around BOSC last
> week, how to contribute modules, and what is the role of a module
> maintainer. I will send out a more detailed summary on that a bit later.
> 
> Andreas
> 
> 
> On Tue, Jul 7, 2009 at 6:34 AM, Franklin Bristow <fbristow at gmail.com> wrote:
> 
>> Hi everyone,
>> Now that you're all back from ISMB (I hope you all had a good time!) I
>> thought it would be a good time to bring this up.
>>
>> A while back I wrote to the list about an ABIF parser and SCF writer that I
>> had written.  I got some pointers on things to change and I've since made
>> the suggested changes.  Now I was wondering how I should go about getting
>> these files into BioJava....
>>
>> --
>> Franklin
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