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IGV-X v2.19.5-igvx.1

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@Micropeptide Micropeptide released this 12 Aug 07:33
· 18 commits to IGV-X since this release
v2.19.5-igvx.1
8aba3e8

IGV-X v2.19.5-igvx.1 — Release Notes

IGV-X is a customized version of IGV built specifically for
micropeptide's research — Arabidopsis
epigenetics, whole-genome bisulfite sequencing (WGBS) methylation analysis,
and large multi-track sessions. It is designed
around those workflows while remaining fully compatible with standard IGV
sessions and genomics file formats.

IGV-X is a robust, modern fork of the Integrative Genomics Viewer (IGV)
(upstream fork base: 2.19.X stable, commit e2bcf4200). It is fully compatible
with standard IGV sessions and genomics file formats, and adds a hardened
chromosome-name resolution layer, large-session performance work, and a
modernized macOS experience.

New in this release

In-app updates (GitHub release channel)

  • Help > Check for Updates... — IGV-X checks Micropeptide/IGV-X releases
    on GitHub for a newer version and offers a one-click download of the new
    .dmg installer.
  • Optional startup check (off by default): Preferences > Updates (IGV-X) >
    "Check for updates on startup".
  • Version comparison understands the vX.Y.Z-igvx.N release scheme.

Highlights of the IGV-X fork

Chromosome-name resolution (top priority)

  • Fixes the stock IGV 2.19.5 bigWig NullPointerException on TAIR10 WGBS
    sessions: BBFile.getIdForChr() returning null when hundreds of
    methylation bigWigs use Chr1..ChrM against a RefSeq-aliased genome.
    Missing mappings never NPE — they degrade gracefully and diagnose
    honestly.
  • Case-insensitive, alias-aware chromosome resolution across bigWig/bigBed/
    BAM/BED/VCF: Chr1/chr1/CHR1/1/RefSeq accessions/organellar names,
    using genome alias information — never global lowercase conversion,
    never renaming user files.
  • Tools > Diagnose Track/Session... shows exactly how each file's
    chromosomes compare to the loaded genome (exact / case-only / alias-only /
    missing), plus index and resource checks.

Large-session performance (~900 bigWigs)

  • Bounded loading threads, async track loading with honest progress, viewport
    culling, and caching — no more freezing the UI while a big session loads.

Sessions & files

  • Relative session paths by default (relative to the session file).
  • Optional .igvx.json companion metadata; sessions still load if it is missing.
  • Unified smart Open (files + sessions auto-detected) and recent files.
  • Cancel Session Loading — escape a stuck session load and open another.
  • Unsaved-session close confirmation.
  • Bookmarks & gene-region highlights persisted in the session file.
  • Batch track import: File > Open Folder of Tracks... scans subfolders,
    filters by type, multi-select.
  • Arabidopsis (tair10) gene lists — DNA methylation core, RdDM pathway,
    small RNA machinery, histone marks & readers, imprinting/DME, flowering time
    (every AGI verified against TAIR10 GTF).

Navigation & region selection

  • Trackpad two-finger swipe / Magic Mouse pan (configurable sensitivity),
    without breaking vertical scroll.
  • ROI drag-select, multi-track selection (Cmd/Shift-click), data-panel
    selection highlight.
  • Configurable default quantitative-track ranges (e.g. min -5 / max 100)
    in Preferences > Tracks > Default Quantitative Range (IGV-X).

Organize tracks by genotype

  • Tracks > Organize Tracks by Genotype... — group tracks by genotype with
    per-genotype background tint, then order CG → CHG → CHH inside each group
    with consistent context colors across genotypes. Editable, remembered
    rules; optional auto-organize after session/batch loads.

Export

  • High-quality PNG / SVG / PDF export (publication mode, selected tracks
    only, DPI control).

Diagnostics & error recovery

  • Exception dedup / rate-limiting (per-type 60 s cooldown) so repeated errors
    don't spam.
  • Batch command listener preserved (port 60151: new/genome/load).

macOS app

  • Native system menu bar, fullscreen, standard shortcuts, Dock icon,
    window-state memory, accessible dialogs, Retina/HiDPI, information-dense
    dark-friendly UI. App name is IGV-X, own bundle ID, prefs/caches/logs
    separated from stock IGV (~/igvx). Bundled JDK — no Java install needed.

Downloads

  • IGV-X-2.19.5-igvx.dmg — shareable installer (drag to Applications)
  • IGV-X-2.19.5-igvx.zip — same app, zip form
  • SHA256SUMS + version.txt

Compatibility

Standard IGV sessions, .igv_session.xml / .xml, all standard genomics
formats (bigWig, bigBed, BAM, CRAM, VCF, BED, GFF/GTF, WIG, TDF, FASTA,
2bit...). Stock IGV 2.19.5 workflows continue to work; IGV-X adds robustness
and diagnostics on top.

Install notes

  • macOS Apple Silicon (universal build: Apple Silicon; Intel via Rosetta/
    x86_64 build on request).
  • Ad-hoc signed: first launch on another Mac may require right-click → Open →
    Open (Gatekeeper). A Developer ID + notarization pass is planned.

Source

  • Repository: https://github.com/Micropeptide/IGV-X
  • Branch: IGV-X (fork base: upstream 2.19.X, commit e2bcf4200)
  • Full diff vs stock IGV: docs/fork-diff.md · docs/changes-vs-igv.md
  • What's different: docs/whats-different.md · Build: docs/build.md
  • Limitations: docs/limitations.md
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