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Consider support for pairix indexed bgzip files

6

Consider implementing support for pairix indexed bgzip files: https://github.com/4dn-dcic/pairix#pairix This essentially allows bedpe files to be 2D indexed. This is likely a solution to any of the arc/rearrangement tracks (provided...

keiranmraine

Have a list of default genomes that users can start with

6

If there was a small list of genome such as human, mouse, arabadopsis, etc to kickstart JBrowse/JBrowse desktop with it might lower barrier to entry

cmdcolin

When using remote data directory in JBrowse desktop, allow saving session still

5

cmdcolin

Save selections hide/unhide across chromosomes Alignments2 track

1

Currently for Alignments2 JBrowse tracks 'Track Visualization types' and 'Coloring options' are saved when navigating across different chromosomes/scaffolds for the same track. Selections made in the 'Hide' checkboxes are not...

bejo-dionnez

error loading bigwig (and other?) files from remote source

22

I have found the following error when trying to load bigwig files. I have no reason to think it's specific to BigWig files, but I haven't yet had the time...

trstickland

The docusaurus docs have ``` table { display:block } ``` This causes messed up rendering  Manually deleting that css fixes it but should probably make jbrowse immune to such...

cmdcolin

ability to "pin" a track to the top of the pane

2

# pin a track to the buttom of the pane In the track menu, have a checkbox menu item called "Pin to top" that makes the track always rendered at...

BioEvo

trackMetadata sources overridden in multiple json config files

1

JBrowse 1.16.3 My configuration files are split across multiple json files so that each contains all the relevant info for a given data set. These include `trackMetadata` such as: ```json...

nathanhaigh

How to get base‘s coordinate when mouse hovers over tracks

2

# How to configure JBrowse to display base's coordinate when mouse hovers over a read in a BAM track when mouse hovers over a BAM track, the blubble will display...

BioEvo

problem loading .bam and .bai files with non-matching names

4

[Note: this was observed in Apollo, but I believe it is related to jBrowse] I encountered a problem trying to load a BAM file, as the index file has a...

trstickland