On Wednesday, October 31, 2012, Edward Hills wrote:

> Thanks Peter.
>
> My next question is, I have found that VCF files don't get split properly
> as the header is not included in the second file as is usually required by
> tools (such as vcf-subset). I have read the code and am happy to implement
> this functionality but am not to sure where this would best be done.
>
> I see a class Text ( data ) which looks like every datatype is sent to.
> Would it be best to implement a VCF class which is called when the datatype
> is VCF?
>
> Cheers,
> Ed
>

VCF is I assume defined as a subclass of Text, so inherits the naive simple
splitting implemented for text files (which doesn't know about headers).

Have a look at the SAM splitting code (under lib/galaxy/datatypes/*.py) as
an example where header aware splitting was done. You'll probably need to
implement something similar.

Peter
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