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Remove bam to bai converter #4598

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merged 1 commit into from Sep 12, 2017

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@mvdbeek
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commented Sep 12, 2017

This converter served no real purpose (you can download bam index files
by clicking on the floppy icon of a bam dataset, and we never had a bai datatype).

I would still like to get this into 17.09, since otherwise there will be some very abundant warnings in the logs (lot's of galaxy.datatypes.registry WARNING 2017-09-04 15:51:32,659 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam’) whenever galaxy checks if a history item is compatible with a tool input.

Remove bam to bai converter
This converter served no real purpose (you can download bam index files
by clicking on the floppy icon, and we never had a bai datatype).
@jmchilton

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commented Sep 12, 2017

@nsoranzo nsoranzo merged commit c0e2db2 into galaxyproject:dev Sep 12, 2017

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@nsoranzo

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commented Sep 12, 2017

Thanks @mvdbeek for following up on this!

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commented Sep 12, 2017

412f24d was reverted in commit 189abc3

@mvdbeek mvdbeek deleted the mvdbeek:remove_bai_converter branch Jun 12, 2018

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commented Jun 22, 2018

xref #5167, I believe this is what caused that issue, and will need to follow up to see what the right fix is here. Can we just update the data providers to use pysam/bams, without involving .bai?

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commented Jun 22, 2018

See "bai": genome.BamDataProvider, in lib/galaxy/visualization/data_providers/registry.py

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