Release v2.10.0

[cmdcolin]

New file format for synteny tracks - PIF

This release adds a new synteny file format PIF ("pairwise indexed format"). It is essentially a small transformation of PAF ("pairwise mapping format") that allows querying the format using tabix.

Preparing a new PIF file

To prepare a PIF file, you can use the @jbrowse/cli tool:

Old workflow

minimap target.fa query.fa > query_vs_target.paf
jbrowse add-assembly target.fa
jbrowse add-assembly query.fa
gzip query_vs_target.paf # optionally gzip paf
jbrowse add-track query_vs_target.paf.gz -a query,target

New

minimap target.fa query.fa > query_vs_target.paf
jbrowse add-assembly target.fa
jbrowse add-assembly query.fa
jbrowse make-pif query_vs_target.paf # generates pif in same folder
jbrowse add-track query_vs_target.pif.gz -a query,target

Conceptually, the PIF file is just a tabix file that allows querying the PAF from either the query->target or the target->query.

Note: We have not yet improved the amount of data needed to view whole-genome overviews of the whole genome alignment, but we anticipate looking into this soon

Impact of using PIF vs PAF

This screenshot shows the example impact of loading a synteny track in the linear genome view: the indexed PIF track allows only a small amount of data to be downloaded, and so it is rendered much quicker. The data is exactly the same as a PAF file

Share link for the screenshot above https://jbrowse.org/code/jb2/main/?config=test_data%2Fhs1_vs_mm39%2Fconfig.json&session=share-DMGteXDmT3&password=6TIWA

Other new features in this release

• added ability to create highlighted regions from the bookmark widget
• click-and-drag or wheel side-scroll in the 'synteny area' of the linear synteny view. additionally, right context click on synteny features
• added support for lzma compression in CRAM files (via @gmod/cram@v2.0.0)

🚀 Enhancement

• core
  • #4138 Speed up large FromConfigAdapter usages with alternative adapter id calculation (@cmdcolin)
  • #4114 Improve pluginManager.jexl typescript definition (@cmdcolin)
• Other
  • #4135 Split "recently used tracks" local storage keys by view assemblies (@cmdcolin)
  • #4003 Adds the ability to highlight regions using the bookmarks widget (@carolinebridge-oicr)
  • #4123 Remove session.notify after using the Add track workflow (@cmdcolin)
  • #3859 Add new pairwise indexed PAF adapter format with CLI creation workflow (@cmdcolin)
  • #4109 Allow right clicking synteny features (@cmdcolin)
  • #4110 Scroll both panels of the linear synteny view when side scrolling the middle panel (@cmdcolin)
  • #4108 Convert to floating-ui for tooltips for small speedup (@cmdcolin)
  • #4107 Refactors and bundle size improvements (@cmdcolin)
• app-core, core
  • #4134 Add ability to click and drag synteny area of synteny view to side scroll (@cmdcolin)

🐛 Bug Fix

• Other
  • #4137 Fix dotplot axis ticks going out of bounds (@cmdcolin)
• core
  • #4136 Fix "Export SVG" feature in next 14 (@cmdcolin)
  • #4125 Fix internet accounts not being shown in file selector after page refresh and hide HTTP basic internet accounts (@cmdcolin)
• app-core, embedded-core
  • #4121 Fix view menu checkboxes not responding in some cases (@cmdcolin)

📝 Documentation

• app-core, product-core, web-core
  • #4106 Add links between autogen docs (@cmdcolin)

🏠 Internal

• #4103 Add mastodon account to website links (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin) Done in 2.06s.

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This discussion was created from the release Release v2.10.0.