Rduckhts 1.1.6-0.0.2 (2026-04-09)

• Fix test_bam_file_offset: cast COUNT(*) results to INTEGER in SQL so the DuckDB driver returns R integer rather than numeric (BIGINT maps to double in the duckdb R driver), restoring expect_identical assertions.

Rduckhts 1.1.6-0.0.1 (2026-04-09)

• Fix bundled read_hts_index_spans(...) / rduckhts_hts_index_spans(): the span view now returns real chunk rows from CSI/TBI/BAI indexes, including populated bin, chunk_beg_vo, chunk_end_vo, chunk_bytes, seq_start, and seq_end values instead of placeholder NAs; BCF-backed calls also avoid the previous noisy tbx probe warning on .csi indexes.
• Add FILE_OFFSET column to rduckhts_bam() / read_bam(...): exposes the BGZF virtual file offset after each record. Zero runtime overhead (macro over already-open struct fields). Enables ORDER BY FILE_OFFSET in SQL LAG() / LAST_VALUE() window functions to reproduce exact BAM file order for streaming deduplication algorithms. Together with the // integer-division operator and LAST_VALUE(... IGNORE NULLS), this permits exact replication of WisecondorX’s larp/larp2 state machine in pure SQL, confirmed at 0 mismatches across 25,115 non-zero bins on a real NIPT BAM.

Rduckhts 1.1.5-0.0.1 (2026-04-08)

• Fix bundled bcftools_liftover(...) / rduckhts_liftover() cache and realignment hardening: per-thread chain/FASTA contexts are now bounded instead of accumulating for the lifetime of worker threads, and scalar left-alignment no longer reuses stale traceback state after failed/empty alignments.
• Fix bundled read_bam(...) / rduckhts_bam() and read_bcf(...) / rduckhts_bcf() indexed parallel full scans when headers contain leading empty contigs: contig claiming now retries iteratively instead of recursively, and the BAM reader no longer returns an empty chunk after successfully handing off to the next contig.
• Keep the top-level extension README.Rmd examples aligned with direct extension usage: the extension README now renders its example queries through a custom DuckDB SQL knitr engine instead of R/DBI, and its liftover example uses bundled fixtures rather than temporary R-generated FASTA/chain files.
• Fix bundled Windows GNU CMake builds: the vendored htslib configure step now distinguishes windows_amd64_mingw from windows_amd64_rtools; the MinGW path keeps the smaller configure.win-style library set, while the Rtools path restores the fuller static libcurl dependency closure required by its htslib feature probes. CURL_STATICLIB remains on the built objects rather than on ./configure test probes.
• Fix bundled Windows windows_amd64_rtools CMake builds: the upstream extension Makefile now pins CC/AR/RANLIB from R CMD config, avoiding mixed non-Rtools compiler and Rtools library selection when vendored htslib is configured; the vendored htslib CMake path also returns to separate configure/build steps on MinGW for simpler diagnostics and behavior, and MinGW static-libcurl builds now define CURL_STATICLIB to match Rtools libcurl.a.
• Fix bundled read_bcf(...) / rduckhts_bcf() mapping of fixed-count INFO/FORMAT arrays: exact-cardinality fields such as Number=2 and Number=4 now materialize as DuckDB array/list columns instead of silently dropping all but the first value.
• Fix bundled read_bcf(...) / rduckhts_bcf() handling of string FORMAT lists such as DRAGEN FORMAT/LAA: Number != 1 string FORMAT fields now materialize as VARCHAR[] instead of triggering DuckDB internal assertion failures.
• Fix bundled duckdb_munge(...) / rduckhts_munge() multithreaded FASTA lookups: FASTA index handles are now thread-local and FASTA fetches are synchronized in munge, avoiding intermittent fai_retrieve failures and aborts when fasta_ref is used with PRAGMA threads > 1.
• Add rduckhts_score(): polygenic risk score computation backed by the bcftools +score plugin, supporting GT/DS/HDS/AP/GP/AS dosage modes, all major GWAS summary presets (PLINK, PLINK2, REGENIE, SAIGE, BOLT, METAL, PGS, SSF/GWAS-SSF), GWAS-VCF multi-PRS scoring, p-value thresholding, sample subsetting, and region/filter controls.
• Add rduckhts_munge(): GWAS summary statistics normalization backed by bcftools +munge, with FASTA reference allele resolution, swap-aware effect/frequency transforms, and METAL meta-analysis column support.
• Add rduckhts_liftover(): variant coordinate liftover backed by bcftools +liftover using UCSC chain files, with full indel normalization, INFO/END lifting, and MT passthrough.
• Add rduckhts_bed() for BED3–BED12 interval files and rduckhts_fasta_nuc() for nucleotide composition over BED intervals or fixed-width bins.
• Add compression and index helpers: rduckhts_bgzip(), rduckhts_bgunzip(), rduckhts_bam_index(), rduckhts_bcf_index(), and rduckhts_tabix_index().
• Add HTS metadata readers: rduckhts_hts_header(), rduckhts_hts_index(), rduckhts_hts_index_spans(), and rduckhts_hts_index_raw().
• Add quality encoding controls to rduckhts_bam() and rduckhts_fastq() (quality_representation, input_quality_encoding) and rduckhts_detect_quality_encoding() for heuristic FASTQ encoding detection.
• Add sequence_encoding := 'nt16' parameter to rduckhts_bam(), rduckhts_fasta(), and rduckhts_fastq() for raw htslib nt16 sequence output as UTINYINT[].
• Add SAM flag helpers sam_flag_bits() and sam_flag_has(), CIGAR utility functions, and is_forward_aligned().
• Bundle duckhts 1.1.5 extension.

Rduckhts 0.1.3-0.0.2.9000

Rduckhts 0.1.3-0.0.2

• Conditionaly enable plugins in windows

• Updates the configure script to avoid check faillure on CRAN MacOS

• Update the extension version to 0.1.3

Rduckhts 0.1.2-0.1.5

• Fixed inadvertant removal of libexec
• Updated the plugin to add header table functions

Rduckhts 0.1.2-0.1.4

• CRAN Submission

Rduckhts 0.1.2-0.0.9000

• Different fixes for CRAN submission
  • Updated DESCRIPTION Title/Description formatting and added HTSlib reference.
  • Removed default write paths in bootstrap/build helpers; now require explicit paths.
  • setup_hts_env now accepts an explicit plugins_dir parameter.
  • duckhts_build now accepts a make argument (GNU make required).
• modified configure to attemp to support wasm
• Update bootstrapped extension code to match duckhts 0.1.2.
• Add SAMtags + auxiliary tag support (standard_tags, auxiliary_tags).
• Add tabix header/typing options (header, header_names, auto_detect, column_types).

Rduckhts 0.1.1-0.0.3

• make the build single threaded

Rduckhts 0.1.1-0.0.3

• misspeling correction

Rduckhts 0.1.1-0.0.2

• CRAN resubmission: apply DuckDB C API header patch to avoid strict-prototypes warnings.

Rduckhts 0.1.1-0.0.1

• CRAN Submission

• Bump bundled duckhts extension version to 0.1.1.

• Initial development release.

• Bundles the DuckHTS DuckDB extension and htslib for HTS file readers.

• Adds table-creation helpers for VCF/BCF, BAM/CRAM, FASTA/FASTQ, GFF/GTF, and tabix.