Changelog

RGenomeTester4 0.2.0

Highlights

• Refactored the niptmer scoring implementation into a thinner exported API plus explicit internal model stages to reduce legacy drift and make the port easier to verify.
• Added file-oriented niptmer workflow utilities for the legacy sample-level contract:
  • niptmer_make_sample_list(),
  • niptmer_count_sample_list(),
  • niptmer_bind_count_table(),
  • niptmer_write_zscore(),
  • niptmer_write_xya(),
  • niptmer_run_sample().
• Replaced the legacy add_rows.pl counting step with a native R implementation built on bundled GenomeTester4 wrappers.
• Added internal paired-FASTQ handling in niptmer_make_sample_list() so the package concatenates multiple FASTQs for one sample before list generation, matching the pipeline contract.
• Made niptmer_interpret() sex chromosome call thresholds configurable via sex_call_spec instead of keeping the legacy values hardcoded in the public function body.

Quality and Compatibility

• Added early validation for duplicated sample identifiers in prepared count tables and coverage matrices.
• Expanded tinytest coverage for the file-oriented niptmer workflow, including artifact writers, duplicate/shape failures, wrapper cleanup behavior, paired FASTQ parity, and end-to-end GT4-backed sample execution.
• Regenerated README examples so the documented niptmer usage now shows the step-level utilities and the thin end-to-end wrapper.

RGenomeTester4 0.1.0

Highlights

• Added processx wrappers for bundled GenomeTester4 binaries (glistmaker, glistcompare, glistquery, gmer_counter, gmer_caller, gassembler).
• Added wrappers for bundled GenomeTester4 Perl scripts (including repeats helpers and patched MakeIntersection.pl/MakeUnion.pl runtime binary lookup).
• Added stateless NIPTmer scoring utilities, including interpretation and control-reference selection helpers.
• Added reference panel building API:
  • import/build panel,
  • VCF and BED blacklists,
  • block-pooled stability whitelist,
  • panel whitelist application and QC summaries,
  • orchestration (niptmer_ref_build).
• Added overlap-aware VCF expansion mode (engine = "legacy_compatible") and ULCWGS tuning profile helper (niptmer_ref_profile_ulcwgs()).

Quality and Packaging

• Added extensive tinytest coverage for wrappers, scoring, reference selection, semantic reference-building behavior, and processx buffer safety.
• Added routine registration and dynamic symbol restrictions in src/init.c.
• Refined README into fully runnable, evaluated examples from README.Rmd.
• Added Windows build support scripts (configure.win, cleanup.win) and executable lookup improvements for .exe binaries.