Release v1.7.10

[cmdcolin]

We are pleased to present the latest JBrowse 2 release!

This has some great new features including

• Feature detail formatters - add callback to add links or other customizations
  to the feature details panels (see
  https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels
  for more info)
• Session URL formats for loading spreadsheet, SV inspector, and linear and
  dotplot synteny views (see https://jbrowse.org/jb2/docs/urlparams/ for details)
• You can enter "chr1 100 200" to navigate to "chr1:100-200" as a simple way to
  copy from a bed file or similar

Feature detail formatter

Here is an example which adds a link to the "Name" panel in the feature
details. It uses the jexl callback that returns an object with keys for each
field to modify (e.g. the key name is used here). See

{
  "type": "FeatureTrack",
  "trackId": "ncbi_gff_hg19_2",
  "name": "NCBI RefSeq",
  "formatDetails": {
    "feature": "jexl:{name:'<a href=https://google.com/?q='+feature.name+'>'+feature.name+'</a>'}"
  },
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz.tbi"
      }
    }
  }
}

Example screenshot

See https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels for more info

Clearer configuration panel with explicit "Add item" button with "OK"/"Cancel" to confirm

Large track menus no longer disappear off the screen

Before

After

Automatically generate clickable links for data files in About track dialog

See also the "Copy config" button to download the config

🚀 Enhancement

• Other
  • #3025 Add dotplot session spec (@cmdcolin)
  • #2975 Add simplified URL format for loading synteny views (@cmdcolin)
  • #3023 Add error handling in case of invalid OAuth2 configuration used. (@andrzejgrzelak)
  • #3020 Allow choosing trackId when using text-index with --file with --fileId (@cmdcolin)
  • #3016 Allow whitespace separated refname,start,end type locstring (@cmdcolin)
  • #3006 Add string array configuration slot UI improvements (@cmdcolin)
  • #2998 Avoid rendering offscreen contents in pileup renderer (@cmdcolin)
  • #3000 Add reference base and correct percentage calculations to tooltip on SNPCoverage display (@cmdcolin)
• core
  • #2981 Add simplified URL format for loading spreadsheet and SV inspector (@cmdcolin)
  • #2990 Use shortened megabases (M) display when zoomed out, and option to hide the "open track selector" button (@carolinebridge-oicr)
  • #3003 Add ability to run field formatters on the feature details panel (@cmdcolin)
  • #3017 Add button to copy track config in About track dialog (@cmdcolin)
  • #2999 Generate clickable links to track data in about track dialog (@cmdcolin)
• __mocks__, core
  • #3005 Use cascading menu helper library for track menu to avoid menu going offscreen (@cmdcolin)

🐛 Bug Fix

• Other
  • #3021 Fix mouseover display of read name to alignments track (@cmdcolin)
  • #3012 Small fix to rankSearchResults logic (@cmdcolin)
  • #3009 Add jsdom to jbrowse-img to fix --noRasterize option (@cmdcolin)
• core
  • #3007 Fix read vs ref dotplot view (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• @andrzejgrzelak

---

This discussion was created from the release Release v1.7.10.