Changes in version 2025-09-02 (2025-09-02) - support passing additional track options to igv.js Changes in version 2025-09-01 (2025-09-01) - migrate from RUnit to testthat Changes in version 2024-08-29 (2024-08-29) - fix issue with loading bed files when app is run with query strings Changes in version 2024-08-25 (2024-08-25) - switch from Rcurl::url.exists to httr::http_error (Windows compatibility) - stop using Amazon S3 URLs by default Changes in version 2024-08-16 (2024-08-16) - fix issue with VCF files Changes in version 2024-08-10 (2024-08-10) - fix issue with custom files not working properly - sync with Bioconductor (3_19 release) Changes in version 2024-04-23 (2024-04-23) - change file links from igv-data.systemsbiology.net to gladki.pl/igvr Changes in version 2024-03-16 (2024-03-16) - add shinytest2 for igvShinyDemo-GFF3.R Changes in version 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 Changes in version 2024-02-28 (2024-02-28) - add pkgdown content Changes in version 2024-02-16 (2024-02-16) - fix bug in function loadBamTrackFromLocalData - improvge way of loading BAM files - show mismatches Changes in version 2024-02-09 (2024-02-09) - fix some Bioconductor NOTEs Changes in version 2024-02-05 (2024-02-05) - fix some Bioconductor NOTEs Changes in version 2024-02-04 (2024-02-04) - make the first Bioconductor release Changes in version 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) Changes in version 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 Changes in version 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 Changes in version 1.9.39 - Prevent the getting-started vignette from reaching gladki.pl while the package builds (#158) Changes in version 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) Changes in version 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 Changes in version 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) Changes in version 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) Changes in version 1.9.34 - Rename the tair10 gene track to the registry name, breaking removeTracksByName on the old label (#143) Changes in version 1.9.33 - Fix the off-by-one start in currentGenomicRegion, closing its round trip through showGenomicRegion (#126) Changes in version 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) Changes in version 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 Changes in version 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 Changes in version 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) Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 1.9.20 - Fix getGenomicRegion() in a shiny module whose id is not igv Changes in version 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 Changes in version 1.9.17 - Enforce green CI on macOS and Windows by dropping the allow-failure matrix flags Changes in version 1.9.16 - Add a getting-started vignette covering the widget, track loaders, navigation and modules Changes in version 1.9.15 - Fix the 404 on locally written tracks when the tracks directory moves Changes in version 1.9.14 - Allow igvShiny() to build outside a shiny session, for scripts and vignettes Changes in version 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 Changes in version 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) Changes in version 1.9.11 - Enable the covr coverage step on every Linux CI build (M3) - Add covr to Suggests Changes in version 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 Changes in version 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) Changes in version 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) Changes in version 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) Changes in version 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 Changes in version 1.9.5 - fix: pass tracks startup option through to igv.js (#36, thanks @M4teuszzGl4dki) Changes in version 1.9.4 - fix: pass autoscaleGroup through in loadBedGraphTrackFromURL (#105, thanks @M4teuszzGl4dki) - fix: support string-based autoscaleGroup values in both bedGraph handlers Changes in version 1.9.3 - ci: fix Windows/macOS CI failures (install pkgload alongside pkgdown) - ci: add automated push to Bioconductor devel on merge to master Changes in version 1.9.2 - fix(ci): add testthat to Suggests field in DESCRIPTION to fix warning Changes in version 1.9.1 - fix(ci): remove missing test_igvShiny_package.R from Collate field to fix build error Changes in version 1.9.0 - Version bump due to Bioconductor 3.23 devel synchronization.