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Hi Andrea,<br>
<br>
Yes, the default behavior in 61 is the same as pre-61, i.e. no
failed variations returned. It's not strictly true to say that any
methods that return multiple objects filters out failed variations
though, if you get multiple objects by a call that explicitly
specifies a list of objects to fetch (e.g.
fetch_all_by_VariationFeatures on TranscriptVariationAdaptor or
fetch_all_by_name_list on VariationAdaptor), you will get the failed
variations irrespective of what the flag on the DBAdaptor says.<br>
But the 'unspecific' fetch methods (e.g. fetch_all_by_Slice,
fetch_all_by_Population etc.) will exclude the failed ones by
default. Also, a minor detail: you don't specify the flag on the
object adaptor but on the db adaptor, i.e.
$obj_adaptor->db->include_failed_variations() (since it's a
global property that affects all object adaptors created for the
connection).<br>
<br>
I hope this is clear <br>
/Pontus<br>
<br>
<br>
On 10/02/2011 00:01, Andrea Edwards wrote:
<blockquote cite="mid:4D532AF0.6000400@cs.man.ac.uk" type="cite">
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Hi Will<br>
<br>
Just to be 100% clear about this answer, are you saying that
methods that return more than one object don't return failed
variants (in v61 and all previous versions) but in v61 you can
call the method include_failed_variations on the adaptors? If i am
reading that right you dont need to check the data returned by the
adaptors for failed variants as they are excluded by default.<br>
</blockquote>
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