v1.0.2

v1.0.2 - 2026-05-25

Fixed

• DELLY writer: FORMAT field order corrected from …FT:RC:RCL:RCR… to …FT:RCL:RC:RCR… to match real DELLY 1.x output; sample column values reordered accordingly so RC stays the SV-region count and RCL/RCR the left/right control regions.
• Manta writer: DUP records now emit <DUP:TANDEM> as ALT (matching the ##ALT declaration in the Manta header) instead of the undeclared <DUP>.
• DELLY writer: BND records now use the standard VCF 4.2 breakend notation (e.g. ]chr3:151368767]C) instead of the symbolic <BND> allele, matching real DELLY output.
• Sampler: SV anchor REF base is now drawn uniformly from A/C/G/T per record instead of being hardcoded to N. This makes BND ALT strings look like G]chr1:42] instead of N]chr1:42].

Added

• README "Scope & limitations" section documenting which INFO/FORMAT fields are declared in the bundled headers but not (yet) populated, split by caller (Manta vs DELLY).

v1.0.1

v1.0.1 - 2026-04-28

Fixed

• gen-pair now produces a two-sample somatic VCF (#7).
• VCF output is now tabix-indexable; previously inter-chromosomal BND records broke sort order (#6).
• README DOI and license badges (#8, #9).

Changed

• BREAKING: gen-pair replaces --out-tumor / --out-normal with a single --out flag.

v1.0.0 — Initial release

[1.0.0] — 2026-04-25

Initial release.

• svforge gen and svforge gen-pair to generate synthetic VCFs (single-sample or coherent tumor/normal pair)
• Manta (VCFv4.1) and DELLY (VCFv4.2) writers
• Injection via --gnomad-fraction and --blacklist-fraction
• INFO/SVFORGE_SOURCE tag on every record (bank / gnomad / blacklist) for self-verifying pipelines
• svforge validate to confirm injected records match the bundled catalogs exactly
• Chromosome filtering via --chromosomes
• Custom header support via --header-template PATH
• Deterministic sampling via --seed; effective seed always logged in the output VCF
• BCF / VCF.gz / VCF output formats
• Default hg38 SV bank with weighted templates across DEL, DUP, INV, INS, BND
• Writer plugin system: third-party callers can register via svforge.writers entry point
• Non-configurable ##svforgeWarning=SYNTHETIC_DATA_DO_NOT_USE_FOR_CLINICAL_DIAGNOSIS injected in every VCF header
• sanitize_command() strips absolute paths from the logged command line so user home directories and cluster paths never leak into generated VCFs
• Python 3.10+, hg38 only