Swift SeqTrace

A native, Swift-based sequence trace editor for fast and reliable DNA data analysis. Inspired by the classic SeqTrace project.

First milestone: open an .ab1 (ABIF) file and render the chromatogram traces.

System requirements

• Minimum macOS: 13 (Ventura) or later. This matches platforms: [.macOS(.v13)] in Package.swift and the SwiftUI APIs used in the app.
• Hardware: Apple Silicon (arm64) and Intel (x86_64) Macs that can run Ventura or newer. Release builds can be shipped as a universal binary (both architectures in one app) so a single download runs on either CPU.
• Note: The minimum OS version is the same for universal and single-architecture builds; “universal” only means both CPU types are included, not a different macOS floor.

Open in Xcode

• Open Xcode
• File → Open… → select the project folder (the one containing Package.swift)
• Press Run

Build a DMG for the lab

From the repository root (full Xcode recommended if you want a universal Intel + Apple Silicon binary):

./scripts/make-dmg.sh

• Output: dist/SwiftSeqTrace-<version>-b<build>.dmg (version and build are read from Sources/SeqTraceMac/AppInfo.swift). The disk image contains Swift SeqTrace.app.
• First open: if the app is only ad-hoc signed, recipients may need Control-click → Open once.
• Universal binary: run with BUILD_UNIVERSAL=1 ./scripts/make-dmg.sh on a Mac that has Apple’s xcbuild (full Xcode install). Otherwise the script builds for your Mac’s architecture only.

Help, About, and internal releases

• User guide (bundled): Sources/SeqTraceMac/Resources/USER_GUIDE.md — copied into the app; testers can open it via Help → Swift SeqTrace User Guide (⇧⌘?).
• About: Swift SeqTrace → About Swift SeqTrace shows version, build, description, and feedback from AppInfo.swift.
• Dock icon: a waveform SF Symbol is applied at launch as a placeholder until you add a real icon (.icns / asset catalog in your shipping app bundle).
• Each internal drop: bump AppInfo.marketingVersion / AppInfo.build, set AppInfo.feedbackContact, and ship the DMG or zip with a name that includes version + build.

GitHub Releases

Published builds live under Releases. For a new version: bump AppInfo, run ./scripts/make-dmg.sh, commit and push, then tag and publish (example with GitHub CLI gh):

git tag -a v0.1.1 -m "Swift SeqTrace 0.1.1 (build 1)"
git push origin v0.1.1
gh release create v0.1.1 "./dist/SwiftSeqTrace-0.1.1-b1.dmg" --repo popollz/SqTr \
  --title "Swift SeqTrace 0.1.1 (build 1)" --notes "Short release notes here."

Current status

File handling

• Opens .ab1 files using an Open Panel (single trace or forward + reverse pair for contig assembly).
• Picks the best 4-channel DATA set (prefers DATA9..DATA12; falls back to DATA1..DATA4 or the largest consistent set).
• Maps channels to bases using the instrument's FWO_1 tag when present; falls back to positional mapping (DATA9=A, DATA10=C, DATA11=G, DATA12=T) when FWO_1 is absent.
• Unit-tested: see Tests/SeqTraceMacTests/ (run with swift test or ⌘U in Xcode).

Chromatogram view (4Peaks-style)

• Dynamic header: shows Base L N, Quality: Q for the currently selected base (color-coded A/C/G/T); shows Base — before the user interacts.
• Top DNA strip of colored base letters above the four traces.
• Quality histogram (pale blue bars behind the traces) with dashed Q20 and Q30 reference lines.
• Translucent blue selection column spanning the full canvas height, with outline on both edges when a range is selected.
• Minimal toolbar: gear popover (Peak-height + Pan), horizontal-zoom slider with N× readout, copy-sequence icon.
• Collapsible Sequence drawer with a full-featured editable NSTextView (closed by default).

Interactions on the canvas

• Click anywhere on the trace → select the nearest base; header + selection column update instantly.
• Click-drag on the trace → pan left/right.
• Pinch (trackpad) → horizontal zoom around the current view center.
• In contig view, clicking either forward or reverse chromatogram moves the consensus caret, which re-highlights both chromatograms in sync.