Hi Peter, thanks again.<div><br></div><div>Turns out that it has been implemented by the looks of it in lib/galaxy/datatypes/tabular.py under class Vcf. However, despite this, it is always the Text class in data.py that is loaded and not the proper Vcf one.</div>

<div><br></div><div>Can you point me in the direction of where the type is chosen?</div><div><br></div><div>Cheers,</div><div>Ed <br><div><br><div class="gmail_quote">On Wed, Oct 31, 2012 at 9:46 PM, Peter Cock <span dir="ltr">&lt;<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>&gt;</span> wrote:<br>


<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br><br>On Wednesday, October 31, 2012, Edward Hills  wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">


Thanks Peter.<div><br></div><div>My next question is, I have found that VCF files don&#39;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.</div>





<div><br></div><div>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?</div><div><br></div><div>Cheers,</div><div>Ed<br>



</div></blockquote><div><br></div></div><div>VCF is I assume defined as a subclass of Text, so inherits the naive simple splitting implemented for text files (which doesn&#39;t know about headers).<span></span></div><div>


<br></div>
<div>Have a look at the SAM splitting code (under lib/galaxy/datatypes/*.py) as an example where header aware splitting was done. You&#39;ll probably need to implement something similar.</div><span><font color="#888888"><div>


<br></div><div>Peter</div>
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