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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
207 stars 62 forks source link

Long read CRAM track produces bad layout in certain case #1654

Closed cmdcolin closed 3 years ago

cmdcolin commented 3 years ago

This is a random thing I stumbled on using minion cram data

There is something weird going on here where the SNPCoverage track is populated but the PileupTrack is not, and apparently for the CRAM track only. Scrolling around in this area I also saw a populated layout with onhover mouse over shadows, but when clicked, it have an error with feature.toJSON being called on undefined feature

cmdcolin commented 3 years ago

Tentatively re-opening as I have found a bad layout again

http://s3.amazonaws.com/jbrowse.org/code/jb2/master/index.html?config=test_data%2Fconfig_demo.json&session=share-fVlQIJG-aO&password=iouXH

This file passes samtools quickcheck

samtools quickcheck https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg002/HG002_ONTrel2_16x_RG_HP10xtrioRTG.cram && echo 'all ok' || echo 'fail'

cmdcolin commented 3 years ago

localhost_3000__config=test_data%2Fconfig_demo json session=local-Cg5fipHMJ (1)

Screenshot of this region

we could try again as a first step to verify this file but the behavior seems weird

cmdcolin commented 3 years ago

Again, note that SNPCoverage is rendered but the pileup is not

cmdcolin commented 3 years ago

igv.js may have issue also https://tinyurl.com/y72bfsps it presents a blank screen

igvjs

igv proper seems ok

Screenshot from 2021-02-18 15-01-32

cmdcolin commented 3 years ago

possible (probable) fix here :) https://github.com/GMOD/cram-js/pull/84

cmdcolin commented 3 years ago

I went ahead and merged https://github.com/GMOD/cram-js/pull/84 (e.g. the linear scan) and released as @gmod/cram 1.5.9 after https://github.com/GMOD/cram-js/pull/85 was found to be flawed in 1.5.8. I put the change into master branch here. I believe it will be solid, if there are concerns we can possibly revisit on @gmod/cram repo...