Restore missing YFull markers for ~12,000 deep clades (e.g. E-Z15929)

Commit 6e50d75 filtered YFull positions to SNP names present in v14 snp_map.txt
to remove ISOGG-only markers, but this also dropped the gap-fill markers (whose
names are not in snp_map.txt), re-orphaning ~9,270 tree nodes — including
E-Z15929/E-FT6657 — so the YFull tree could no longer resolve them.

Restore those markers additively across hg38/hg19/t2t from the last good state
(d4fbd18): rows for currently-orphaned haplogroups, clean SNPs only (indels and
ISOGG SNPs excluded). hg38 orphaned nodes drop 13,080 -> 739. Existing rows are
untouched, so the ISOGG-removal that fixed mixture false-vetoes is preserved.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Yleaf v4.1.3

- Data-loss fix: refuse to run when the output folder is the input folder (or contains it)
- Portable (no-install) dashboard zips for Windows, macOS and Linux
- Documentation + version bump to 4.1.3

Yleaf v4.1.2 — ISOGG ~ fix + dashboard multi-input

- ISOGG ~ markers excluded from all QC; positions regenerated with ~ preserved
- Browse file accepts multiple inputs (staged into a temp dir)
- Mixed-type directories fan out one job per type

Yleaf v4.1.1 — UYSD iframe + UX patch

- Fix UYSD haplogroup-map iframe on Windows (Tauri now uses https://tauri.localhost)
- Reset all form fields when "+ New" is clicked
- Correct "Yleaf 4.0" → "Yleaf 4.1" in window title and home header
- Cargo.lock brought in sync with package version

Yleaf v4.1.0

fix(vcf): case-insensitive chrY replacement in BED for VCF pipeline

Position BED files use 'chry' (all lowercase); the chromosome rename
used line.replace("chrY", ...) which is case-sensitive and found
nothing, leaving the temp BED with 'chry' while VCFs use 'chrY'.
bcftools view -R then matched no positions, producing an empty
filtered VCF → empty bcftools query output → EmptyDataError.

Fix: replace both casings so all BED files (old 'chrY' and new
'chry' format) are normalised to the VCF's actual chromosome name.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Yleaf v4.0.1

- fix(isogg): correct inverted GHIJK trunk and remove parser artifacts (closes #52)
- fix(isogg): restore missing K-subtree intermediate nodes
- ci: build minimap2 from source on Windows; hard-fail if a required tool is missing

fix: add opener:allow-open-path permission to open tree HTML files

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Merge pull request #23 from genid/v3.2.1

Added functionalities for working with ancient DNA, and automatic pai…

Merge pull request #22 from genid/v3.2

V3.2