Bug? Balloon hover callback being called with 2 different objects

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Bug? Balloon hover callback being called with 2 different objects

Keiran Raine
Hi,

I'm currently building a new GBrowse instance with v2.55 and after copying across our old callback module I've found that I'm getting odd errors when call-backs are run on BAM track elements like:

An error occurred while evaluating the callback at section='812_PD4107a_bwa', option='balloon hover':
   => Can't locate object method "flag" via package "Bio::SeqFeature::Lite"

I did some digging and the problem that appears to be occurring is that the call back is being called twice once with the expected BAM object:

Bio::DB::Bam::AlignWrapper

and then again with the unexpected:

Bio::SeqFeature::Lite

I've prevented the spamming of my error logs by adding the following to the beginning of my call back:

return unless($f->can('flag'));

I'm guessing that this is creating additional unnecessary load on the server so probably worth investigating.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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