• Restore missing YFull markers for ~12,000 deep clades (e.g. E-Z15929)
• docs: document --no-ref-inference flag and bump download filenames to 4.1.4
• chore(release): bump version to 4.1.4
• Handle recurrent (homoplastic) Y-SNPs: keep in output, exclude from QC
• Add --no-ref-inference flag to skip reference fallback for panel VCFs

• chore(release): bump version to 4.1.3
• docs: document portable dashboard zips and refresh download filenames to 4.1.3
• ci: add portable (no-install) dashboard zips to release for Windows/macOS/Linux
• Add output/input overlap guard to prevent input data deletion

Yleaf v4.1.2

• ISOGG ~ (approximate-placement) markers no longer count toward any QC score; regenerated isogg_positions_{hg19,hg38,t2t}.txt preserves the ~ from the source so e.g. R1b1a1b1a1a1~ markers (FGC36477/8/9) no longer drag R1b1a1b1a1a1's QC2 below threshold.
• Dashboard: Browse file accepts multiple inputs in one shot; they are staged into a temp dir (with their .bai/.crai/.csi indexes) and processed by the directory-mode pipeline.
• Dashboard: directories containing multiple eligible input types (e.g. BAM + VCF) now fan out one job per type into <output_dir>/<type>/, instead of silently picking only the highest-priority type.

• chore(release): bump dashboard version to 4.1.1
• fix(dashboard): reset all form fields when New is clicked
• fix(dashboard): force https scheme on Windows for stable UYSD iframe
• fix(dashboard): update window title and header to 4.1

Yleaf v4.1.0

• Dashboard now integrates with the Y-SNP Database (UYSD): embedded haplogroup-frequency maps in the result pane, plus a built-in submission flow.
• VCF input now produces real predictions on whole-genome inputs: reference-based ancestral inference restored, plain .vcf files accepted (resolves issue #54).
• --ref-fasta is validated against --reference_genome and raises a clear error on build mismatch.
• Ancient-DNA position files regenerated as main minus C→T/G→A rows; marker counts roughly double across all builds.
• T2T marker names and chrY reference restored — both were shipping as empty/blank placeholders.
• Python 3.7 compatibility restored for the bundled sidecar.

• fix(vcf): case-insensitive chrY replacement in BED for VCF pipeline
• fix(deps): bump @tauri-apps/api to ^2.11 to match Rust crate 2.11.2
• feat(db): add sample_meta table with get/upsert commands
• feat(dashboard): add embedded UYSD WebviewWindow toggle
• feat(dashboard): add UYSD haplogroup map link button
• chore: bump version to 4.0.2
• chore(deps): refresh Cargo.lock transitives
• chore(deps): bump @sveltejs/kit to 2.61.1 + cookie override 0.7.2
• chore(deps): bump svelte to 5.55.9

• ci: harden Windows staging script for minimap2 + DLL collection
• chore: bump version to 4.0.1
• ci: build minimap2 from source on Windows and hard-fail if missing
• fix(isogg): restore missing K-subtree intermediate nodes
• fix(isogg): correct inverted GHIJK trunk and remove parser artifacts
• ci: upload to existing release instead of failing
• ci: fix malformed YAML in release workflow
• ci: cancel in-progress release runs for the same tag

• Added graphical dashboard (GUI) for Windows, macOS, and Linux — the new primary interface for end users
• Added multi-tree prediction: run YFull, FTDNA, and ISOGG trees in a single command with one shared pileup (-tree yfull ftdna isogg)
• Added YFull v14.01 as the new default tree (~235,000 marker positions), FamilyTreeDNA Y-haplotree, and ISOGG tree support
• Added forensic mixture analysis mode (-mix): detects multiple Y-chromosome contributors, estimates ratios, and assigns a haplogroup per contributor
• Added T2T (CHM13v2.0 / hs1) reference genome support
• Added ancient DNA mode (-aDNA): ignores G>A and C>T post-mortem deamination artefacts
• Added PLINK/SNP-array input (-plink)
• Replaced static PDF haplogroup tree output with an interactive self-contained HTML file (-dh)

What's Changed

• Added functionalities for working with ancient DNA, and automatic pai… by @dionzand in #23

Full Changelog: 3.2...3.2.1

• Included support for vcf files
• Optimized the prediction algorithm by adapting the QC1 value to the Yfull tree
• Added the –cr option for CRAM files
• Added the –pq option to define the prediction quality threshold
• Increased the default –pq to 0.95 making the prediction more stringent
• Resolved compatibility issues when using the –old option