On Thu, Nov 1, 2012 at 1:48 AM, Edward Hills <ehills...@gmail.com> wrote:
> Hi Peter, thanks again.
> Turns out that it has been implemented by the looks of it in
> lib/galaxy/datatypes/tabular.py under class Vcf.

Yes, looking at the Vcf class it lacks a merge method (the Sam class
earlier in the file defines its own - do something similar).

> However, despite this, it
> is always the Text class in data.py that is loaded and not the proper Vcf
> one.

Python inheritance means if the Vcf class it lacks a merge method,
it would call the parent class' method (the Tabular class, if it had one),
or the grandparent class's method (the Text class). So it is falling
back on the Text merge which doesn't know about headers.

(As an aside, I would like the Tabular merge to be a bit more
clever about #header lines, but this isn't trivial as some tabular
files contain #comment lines too.)

> Can you point me in the direction of where the type is chosen?

Your tool's XML should specify the output format - although there
could be complications if for example you are doing a dynamic
format selection based on one of the parameters.

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