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GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
205 stars 61 forks source link

Support PIF format on gui #4565

Closed alpapan closed 1 week ago

alpapan commented 2 weeks ago

could we please allow the user interface to load a PIF via the PairwiseIndexedPAFAdapter?

at the moment when i want to look at synteny, I have to select a PAF and then manually edit the track's config.

cmdcolin commented 2 weeks ago

thanks for making this request, definitely should be added!

cmdcolin commented 1 week ago

made a basic implementation of this in the now released v2.15.3 :)

alpapan commented 1 week ago

yeah! thank you, it works! question: is it better to create a csi or tbi index?

cmdcolin commented 1 week ago

the major difference is that CSI supports indexing larger genomes e.g. where individual chromosomes are larger than 2^29 (~512Mbp) such as wheat (TBI is fundamentally unable to index chromosomes larger than that, BAI for that matter too, which is why BAM sometimes also has CSI index)

there are smaller differences but generally you can use TBI unless you are working on an organism with super long chromosomes