NEWS

---

igvShiny 2025-09-02 (2025-09-02)

• support passing additional track options to igv.js

igvShiny 2025-09-01 (2025-09-01)

• migrate from RUnit to testthat

igvShiny 2024-08-29 (2024-08-29)

• fix issue with loading bed files when app is run with query strings

igvShiny 2024-08-25 (2024-08-25)

• switch from Rcurl::url.exists to httr::http_error (Windows compatibility)

• stop using Amazon S3 URLs by default

igvShiny 2024-08-16 (2024-08-16)

• fix issue with VCF files

igvShiny 2024-08-10 (2024-08-10)

• fix issue with custom files not working properly

• sync with Bioconductor (3_19 release)

igvShiny 2024-04-23 (2024-04-23)

• change file links from igv-data.systemsbiology.net to gladki.pl/igvr

igvShiny 2024-03-16 (2024-03-16)

• add shinytest2 for igvShinyDemo-GFF3.R

igvShiny 2024-03-14 (2024-03-14)

• fix issues with GFF3 data
  • make igvShiny demo app for GFF3 working
  • update trackName of GFF3 (from URL)
  • udpate path to local GFF3

igvShiny 2024-02-28 (2024-02-28)

• add pkgdown content

igvShiny 2024-02-16 (2024-02-16)

• fix bug in function loadBamTrackFromLocalData
• improvge way of loading BAM files - show mismatches

igvShiny 2024-02-09 (2024-02-09)

• fix some Bioconductor NOTEs

igvShiny 2024-02-05 (2024-02-05)

• fix some Bioconductor NOTEs

igvShiny 2024-02-04 (2024-02-04)

• make the first Bioconductor release

igvShiny 1.9.51

• Fix demo BED and bedGraph tables that named chromosome 1 as '1' on hg38, tripping the reference check

igvShiny 1.9.50

• Fix pending-message queue lifecycle across re-render, widget replacement, and failed start (#189)
• Fix error banner escaping for genomeName and error message (#189)
• Add Node.js runtime test harness for widget lifecycle and error handling (#189)

igvShiny 1.9.49

• Fix track loaders dropped when called before the igv browser is ready (#185)

igvShiny 1.9.48

• Fix custom local genomes behind remote servers by serving the fasta and index with HTTP Range support (#183)
• Allow serveLocalFile() to accept a Shiny module session proxy

igvShiny 1.9.47

• Handle remote genome host outages gracefully in igv.js with in-widget error banner and igvError Shiny event (#182)
• Clean shadowRoot and dispose previous browser instances on re-render to prevent stacked duplicate viewers (#182)
• Discard and dispose superseded async browser initializations via render generation tracking (#182)
• Add zero-network offline demo mode (SARS-CoV-2) to the flagship showcase app using bundled data

igvShiny 1.9.46

• Add trackHeight parameter and coverageTrackHeight/showCoverage options for alignment tracks (#174)

igvShiny 1.9.45

• Add pre-flight reference compatibility check with warnings and toasts for BAM, CRAM, VCF, and BED tracks (#179)
• Add checkReferenceCompatibility for offline validation of contig naming, assemblies, and coordinate bounds (#179)

igvShiny 1.9.44

• Add HTTP Range Request streaming for local BAM and CRAM tracks (#174)
• Add serveLocalFile and loadBamTrackFromLocalFile for zero-RAM local alignment streaming (#174)
• Add BAM local file stream to the flagship demo and update local-data demo
• Update inst/extdata/tumor.bam to a GRCh38 alignment sample for clean demo rendering

igvShiny 1.9.43

• Remove the track files a session wrote when that session ends (#152)

igvShiny 1.9.42

• Switch the hg19 and hg38 assets to igv.org, off a hgdownload host answering in tens of seconds (#167)
• Use the tabix-indexed RefSeq annotation, so startup reads the locus rather than the whole genome (#167)
• Fix the demo BAM track, which drew GRCh37 reads against the hg38 reference (#168)

igvShiny 1.9.41

• Split the demo apps so each covers one feature in under sixty lines, adding gff3.R and junctions.R (#64)
• Move the showcase app to inst/showcase, leaving inst/demos for the focused examples (#64)
• Drop the makefile targets naming demo files removed in #156

igvShiny 1.9.40

• Switch the custom genome example to the sarsGenome files the package ships, keeping R CMD check offline
• Wrap the remote GWAS example in donttest, since the GWASTrack constructor checks that the url resolves

igvShiny 1.9.39

• Prevent the getting-started vignette from reaching gladki.pl while the package builds (#158)

igvShiny 1.9.38

• Add loadSpliceJunctionTrackFromLocalData, writing junctions held in R as the bed igv.js reads (#103)
• Support merged tracks in the startup track list, drawing junction arcs over a coverage track (#103)
• Extend the track option allowlist with alpha, the blend a merged track hands its members (#103)

igvShiny 1.9.37

• Add the Track options reference vignette, covering every track type and its options
• Replace the overview vignette, whose content the two remaining vignettes already held
• Move the http custom genome example into the getting started vignette

igvShiny 1.9.36

• Remove 14 track options igv.js never reads, which reached the browser and were ignored (#159)
• Add negColorScale and posColorScale, the gradients seg tracks read (#159)
• Add a test holding the option allowlist to the bundled igv.js build (#159)

igvShiny 1.9.35

• Rewrite the demo apps on bslib, replacing 15 legacy apps with 7 single-topic ones (#64)
• Remove the forked Connect app, which now runs the package demo itself (#64)
• Extend the flagship demo with the splice junction and removeTracksByName calls (#64)

igvShiny 1.9.34

• Rename the tair10 gene track to the registry name, breaking removeTracksByName on the old label (#143)

igvShiny 1.9.33

• Fix the off-by-one start in currentGenomicRegion, closing its round trip through showGenomicRegion (#126)

igvShiny 1.9.32

• Add loadSpliceJunctionTrackFromURL, drawing STAR splice junctions from a bed file (#103)
• Extend the track option allowlist with the igv.js splice junction filters and labels (#103)
• Fix the dead asset URLs in the bundled igv.js examples, and scan that directory (#103)

igvShiny 1.9.31

• Add loadCramTrackFromLocalData, serving a cram file and its index to igv.js (#102)
• Extend the loader tests with the local cram payload and the staged files

igvShiny 1.9.30

• Allow alignment tracks to sort their reads by a bam tag through trackConfig (#104)
• Add a test pinning the sort object sent to igv.js

igvShiny 1.9.29

• Resolve tair10 through the igv.js registry, dropping the self-hosted fasta (#143)
• Read the rhos sequence and genes from the UCSC assembly hub instead of gladki.pl (#143)
• Remove the hg19 Gencode v18 track, whose s3 bucket answers 403 (#143)

igvShiny 1.9.28

• Fix a second igvShiny widget staying silent at a locus another one already reports (#126)
• Add a headless test moving two widgets on one page to the same region

igvShiny 1.9.27

• Remove the mm10 and danRer11 reference workaround, unneeded with igv.js 3.x (#107)
• Drop four unused igv.js builds and the unreferenced stylesheet from the package
• Read the genome registry igv.js 3.x uses and document the UCSC dependency it carries

igvShiny 1.9.26

• Update the Connect Cloud manifest, which pinned a commit older than the demo
• Expose the installed igvShiny version in the demo sidebar

igvShiny 1.9.25

• Allow a gwas column mapping through trackConfig, for loadGwasTrack callers
• Extend the Connect Cloud demo with a gwas track using custom columns and colors

igvShiny 1.9.24

• Send the gwas column mapping to igv.js, so any data frame layout works (#32)
• Support a chromosomeColorMap argument coloring gwas points per chromosome (#46)
• Prevent out-of-range gwas column numbers from yielding a silently empty track

igvShiny 1.9.23

• Restore the full three-system matrix on every pull request
• Remove the full-ci label, redundant once macOS and Windows finish in minutes
• Correct the macOS libxml2 config path, wrong since the runners moved to arm64

igvShiny 1.9.22

• Reduce the pull request matrix to Linux, running macOS and Windows on master and nightly
• Enable a full-ci label to force the whole matrix on a pull request

igvShiny 1.9.21

• Bump the GitHub Actions used in CI to their current major versions
• Replace the mutable upload-artifact@master reference with a released version

igvShiny 1.9.20

• Fix getGenomicRegion() in a shiny module whose id is not igv

igvShiny 1.9.19

• Reduce bioconductor.org round trips in CI and cancel superseded pull request runs
• Disable the BiocCheck deprecation lookup, the last CI step reaching bioconductor.org
• Prevent the macOS and Windows jobs from rebuilding every package on each run

igvShiny 1.9.17

• Enforce green CI on macOS and Windows by dropping the allow-failure matrix flags

igvShiny 1.9.16

• Add a getting-started vignette covering the widget, track loaders, navigation and modules

igvShiny 1.9.15

• Fix the 404 on locally written tracks when the tracks directory moves

igvShiny 1.9.14

• Allow igvShiny() to build outside a shiny session, for scripts and vignettes

igvShiny 1.9.13

• Prevent NA or empty names in trackConfig, warning instead of erroring
• Enforce a non-empty scalar string for the startup track url

igvShiny 1.9.12

• Add unit tests for the track loaders, driven by a fake Shiny session (M3)
• Replace the gladki.pl test fixtures with a local httpuv static server
• Extend test coverage from 16% to 92% (M3)

igvShiny 1.9.11

• Enable the covr coverage step on every Linux CI build (M3)
• Add covr to Suggests

igvShiny 1.9.10

• Wrap the 25 over-long lines in R/igvShiny.R at 80 characters (BiocCheck)
• Move paste() out of warning() calls, keeping the message text unchanged
• Exclude local *.BiocCheck/ output folders from git

igvShiny 1.9.9

• Bump the bundled igv.js from 2.13.1 to 3.8.4 (minified) and update the locuschange handler for the 3.x event payload — it now reads the locus from the referenceFrameList and keeps the whole-genome "all" view working (#116)

igvShiny 1.9.8

• Add labels to all vignette code chunks (BiocCheck)
• Add the R Consortium fnd (funder) role to Authors@R — the ISC grant funding this work (BiocCheck)

igvShiny 1.9.7

• Add a public, clickable demo app deployed on Posit Connect Cloud, plus the repository's first README (#117, #118)
• Add a modern bslib (Bootstrap 5) UI to the Connect demo — grouped controls, themed layout, IGV viewer in a full-screen-able card (#119)

igvShiny 1.9.6

• docs: credit past contributors in DESCRIPTION — Carolina Heimann, Steffen Klasberg, Vincent Carey, Parv Sachdeva and Mateusz Gladki are now listed as ctb

igvShiny 1.9.5

• fix: pass tracks startup option through to igv.js (#36, thanks @M4teuszzGl4dki)

igvShiny 1.9.4

• fix: pass autoscaleGroup through in loadBedGraphTrackFromURL (#105, thanks @M4teuszzGl4dki)
• fix: support string-based autoscaleGroup values in both bedGraph handlers

igvShiny 1.9.3

• ci: fix Windows/macOS CI failures (install pkgload alongside pkgdown)
• ci: add automated push to Bioconductor devel on merge to master

igvShiny 1.9.2

• fix(ci): add testthat to Suggests field in DESCRIPTION to fix warning

igvShiny 1.9.1

• fix(ci): remove missing test_igvShiny_package.R from Collate field to fix build error

igvShiny 1.9.0

• Version bump due to Bioconductor 3.23 devel synchronization.