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Published 20 hours ago • verified publisher icon GMOD

BAM store sequenceAdapter cannot be edited in the GUI

Open rbuels opened this issue 4 years ago • 4 comments

When you edit the config of a track with a BAM adapter, the sequenceAdapter slot comes up as null in the GUI.

image

@cmdcolin indicated in grooming just now that this may have something to do with types.late not quite working for this, and the sequenceAdapter having to be a types.frozen. CRAM, in contrast, has this config slot as an AnyDataAdapterConfig slot type, which is probably the right thing to use here if it can be made to work.

rbuels avatar Aug 28 '20 18:08 rbuels

pluginManager.pluggableConfigSchemaType('adapter')

rbuels avatar Aug 28 '20 18:08 rbuels

It is not necessarily true that it cannot be edited in the GUI but that it is frozen so it is a JSON blob

See

t1

cmdcolin avatar Aug 28 '20 19:08 cmdcolin

Using https://github.com/GMOD/jbrowse-components/tree/bam_nonfrozen_seqadapter

Uncaught Error: invalid config slot definition for BamIndex.indexType: Maximum call stack size exceeded

Instantly get this error after running

cmdcolin avatar Aug 28 '20 20:08 cmdcolin

Ultimately we would like to make it so that sequence adapters can be gotten automatically and not be part of the config.

Failing that, let's at least make it editable nicely in the GUI like the one for the CRAM adapter is.

rbuels avatar Sep 04 '20 18:09 rbuels

currently edit it as json...would recommend auto-supplying from current assembly as alternative to working on this

cmdcolin avatar Nov 17 '22 23:11 cmdcolin