@jbrowse/cli - npm Package Versions

2.16.0 (2024-10-23)

:rocket: Enhancement

• Other
  • #4615 Add configuration of transcriptTypes and containerTypes to the svg feature rendering (@cmdcolin)
• app-core, core
  • #4430 Multi-level synteny rendering (@cmdcolin)

:bug: Bug Fix

• Other
  • #4593 Fix navigating to a refname result that is also indexed in search track index (@cmdcolin)
  • #4612 Fix error with tooltips in embedded components in vite dev mode (@cmdcolin)
  • #4602 Fix decoding of CRAM ML tag (@cmdcolin)
  • #4594 Fix highlight button causing issues clicking underlying track features (@cmdcolin)
  • #4586 Update electron-builder to fix broken desktop builds (@cmdcolin)
• core
  • #4600 Fix check for "hasSubSubfeatures" in svg feature rendering (@cmdcolin)
  • #4590 Fix opening .jbrowse files on desktop (@cmdcolin)

:memo: Documentation

• #4607 Add tiberius sample dataset and updated gencode and ncbi GFF gene sets (@cmdcolin)

:house: Internal

• Other
  • #4607 Add tiberius sample dataset and updated gencode and ncbi GFF gene sets (@cmdcolin)
• app-core, core, embedded-core, product-core, web-core
  • #4606 Remove react-error-boundary (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.02s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.4

2.15.4 (2024-09-20)

:bug: Bug Fix

• Other
  • #4582 Fix text indexing on Windows (@cmdcolin)
• text-indexing
  • #4580 Fix indexing plaintext gff/vcf on desktop (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.22s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3

Done in 0.57s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2

2.15.2 (2024-09-18)

:rocket: Enhancement

• #4573 Add pif.gz option to synteny import form (@cmdcolin)

:bug: Bug Fix

• #4571 Fix code signing on the windows for jbrowse desktop (@cmdcolin)
• #4566 Fix handling of "." in VCF ALT field (@cmdcolin)

:house: Internal

• #4569 Refactor GFF3 parser to avoid returning internal _linehash variable (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.30s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.1

2.15.1 (2024-09-12)

:rocket: Enhancement

• core, sv-core
  • #4561 Create notion of launching a single-row breakpoint split view (@cmdcolin)
• Other
  • #4556 Add dropdown menu from bookmark label clicks (@cmdcolin)
• core
  • #4554 Fix the ability to sort menu items by priority for CascadingMenu (@cmdcolin)

:bug: Bug Fix

• Other
  • #4560 Fix coloring on circular chord renderings (@cmdcolin)
• core
  • #4553 Fix performance regression since v2.14.0 in assembly loading (@cmdcolin)

:house: Internal

• core
  • #4548 Create BaseTooltip component in @jbrowse/core/ui (@cmdcolin)
• Other
  • #4547 Avoid stream polyfill for GFF3/GTF parsing (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.16s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.0

Done in 1.26s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.14.0

2.14.0 (2024-08-28)

:rocket: Enhancement

• core
  • #4532 De-duplicate snackbar messages (@cmdcolin)
  • #4516 Add NCBI sequence_report.tsv alias adapter, with ability to recode NCBI fasta files to use UCSC style names (@cmdcolin)
• Other
  • #4533 Allow setting sequenceType='pep' in ReferenceSequenceTrack configuration (@cmdcolin)
  • #4531 Add UnindexedFastaAdapter for fetching small plaintext FASTA files (@cmdcolin)
  • #4528 Add description config slot to reference sequence track (@cmdcolin)
• app-core, core
  • #4523 Allow plaintext GTF and VCF files greater than 512Mb (@cmdcolin)
• core, product-core
  • #4519 Add "Group by" method for alignments tracks (@cmdcolin)

:bug: Bug Fix

• #4535 Fix crash after navToLocString in some cases (@cmdcolin)

:house: Internal

• Other
  • #4530 Consolidate gff3 adapter featureData routine, avoid Number-ifying null phase (@cmdcolin)
• core
  • #4518 Don't send displayModel to "rendering" components on server side (@cmdcolin)
• __mocks__, app-core, core, embedded-core, product-core, text-indexing, web-core
  • #4513 Add new eslint rules (no-unnecessary-condition, no-unused-expressions, etc) and tsconfig noUncheckedIndexedAccess (@cmdcolin)
• app-core, core, embedded-core, product-core, text-indexing, web-core
  • #4510 Add biome lint fixes (@cmdcolin)
• core, product-core, text-indexing
  • #4508 Use @mui/x-charts-vendor for d3 upgrade (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.30s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.13.1

2.13.1 (2024-07-31)

:rocket: Enhancement

• #4497 Add ability to toggle "Show track outlines" (@cmdcolin)

:bug: Bug Fix

• #4501 Fix opening track selector in linear synteny view causing crash in v2.13.0 (@cmdcolin)
• #4495 Fix log scale for some types of signal tracks (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.30s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.13.0

2.13.0 (2024-07-25)

:rocket: Enhancement

• #4494 Add assembly name to scalebar in synteny views (@cmdcolin)
• #4480 Changes default height for SVG rendering to maxHeight to fix blank track effect on slow CPU (@carolinebridge)
• #4478 Add ability to use CSI indexes in @jbrowse/img (@cmdcolin)

:bug: Bug Fix

• core
  • #4483 Fix configuration settings for track sorting in the track selector (@cmdcolin)
• Other
  • #4476 Fix config editor crash in vite usage of embedded components in dev mode (@cmdcolin)
  • #4473 Fix 'Show no tracks active button' checkbox not working (@cmdcolin)

:memo: Documentation

• core
  • #4481 Add SARS-CoV2 demo to test_data (@cmdcolin)
• Other
  • #4487 Update faq.md with compression explanation (@Maarten-vd-Sande)

:house: Internal

• core
  • #4493 Remove prop-types from re-exports (@cmdcolin)
  • #4492 Change abortable-promise-cache to @gmod/abortable-promise-cache (@cmdcolin)
• Other
  • #4488 Fix autogen docs build (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge)
• Colin Diesh (@cmdcolin)
• @Maarten-vd-Sande Done in 1.66s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.3

2.12.3 (2024-06-27)

:rocket: Enhancement

• #4465 Add contig to the default dontRedispatch list for Gff3TabixAdapter (@cmdcolin)
• #4464 Bump generic-filehandle to put URL in error messages (@cmdcolin)

:bug: Bug Fix

• #4469 Fix error launching session on desktop in v2.12.2 (@cmdcolin)

:memo: Documentation

• #4466 Add demo of using farm-fe bundler for embedded components (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.30s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.2

Done in 0.74s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.1

Done in 0.81s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.0