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Rduckhts 1.5.2-0.1.5

This package bundles DuckHTS 1.5.2.

Sample identity and contamination

• Add a runnable README workflow from bundled VCF FORMAT/AD extraction through packed sketches, relatedness, CHARR, and directional matched contamination.
• Add rduckhts_somalier_import_sites() for converting an already selected sites VCF/BCF into the typed panel and population-frequency relation, with allele and frequency orientation kept together.
• Add rduckhts_somalier_bam_counts() for panel-aligned BAM/CRAM A/B/other extraction with explicit reference/index inputs, read/base filters, overlap policy, resource limits and transport settings. A committed panel relation or Parquet file is prepared once; worker_count controls native DuckDB scan jobs with isolated reader/reference state and bounded hash-indexed overlap names, while decompression_threads separately controls htslib workers per handle. Indexed requests use resolved reference IDs, preserving valid contig names that contain region-expression punctuation. Returned data frames are ordered by site index; caller TEMP panels and uncommitted changes are not visible during retained-connection panel preparation.
• CRAM extraction preserves the alignment file’s original @SQ lengths and accepts a non-colocated explicit FASTA index without creating a default reference sidecar.
• Add rduckhts_somalier_vcf_counts() for complete panel-aligned VCF/BCF FORMAT/AD evidence with exact allele-slot mapping, explicit FILTER policy, unavailable-site rows and source record/sample provenance.
• Add rduckhts_somalier_sketches() and rduckhts_somalier_relatedness() for panel-checked count evidence, reusable packed sketches and selected-pair statistics. Tables or ordinary Parquet files can supply inputs and retain typed results; unavailable count tuples remain distinct from measured zero counts.
• Bundled SQL duckhts_somalier_verify_relatedness() checks persisted pair results against their sealed sketches, including identity, denominators, metrics and nullable numerical status.
• Bundled SQL duckhts_somalier_verify_sketches() rebuilds sketches from retained evidence and detects raw-count or availability changes even when the classified genotype is unchanged. Invalid retained classification settings return false instead of becoming rebuild-aggregate settings.
• Add rduckhts_somalier_charr() and rduckhts_somalier_matched_contamination() over measured count channels and aligned population-B allele frequencies. They retain numerical status and usable-site denominators, and reject changed panel/evidence identity. The matched method preserves receiver/anchor direction and evaluates only requested ordered pairs without a pair-sized native workspace. CHARR results are stable across parallel aggregate reduction order.
• Bound sample and assembly identities retained by bundled sketch, CHARR, and matched-contamination states to 1,024 bytes, including persisted inputs. Panel assembly and region are checked before hash encoding.
• Preserve strict binomial-tail cutoffs with outward-rounded comparisons and a per-call max_threshold_work limit shared across distinct measured depths for both contamination wrappers; exhaustion errors without partial results. Sketches constructed with IEEE negative-zero balance settings round-trip.
• The bundled estimators use stable high-depth CHARR tail evaluation and a full-grid matched search. Their documented numerical counterexamples can differ from Somalier v0.3.4 output; they are not bitwise CLI replicas.

Genotypes and variant readers

• Add rduckhts_geno() for typed arbitrary-ploidy GT/PS calls and rduckhts_bcf_samples() for original-header sample identities. Sample selection retains original sample indices; sparse scans preserve variant records while omitting calls without a called ALT.
• Select extra typed FORMAT fields with format_fields = c("AD", "DP", "GQ"), including values on records without GT. Header types/cardinalities and missing elements remain intact. Single-file and multi-file BCF wrappers also support per-call sample selection.
• Use include_filter = TRUE to retain the same physical VCF/BCF record’s FILTER beside typed calls; PASS, unapplied dot and named failures remain distinguishable without a separate reader join.
• Preserve an unapplied FILTER dot as NULL in bundled read_bcf() rather than reporting it as [PASS].
• Use raw_gt = TRUE to retain exact original VCF genotype text, including leading phase markers and literal missing alleles. BCF rejects this option because it does not store the original text.
• Preserve CSQ/ANN/BCSQ on every tidy sample row, selected-sample PS values with BCF padding, and HTSlib’s VCF 4.4 genotype phase spelling. Malformed numeric scalar INFO/FORMAT fields follow decode_error_policy rather than being silently truncated.
• Preserve duplicate records, literal colon-bearing contigs and indexed VCF records absent from a partial header. Prepared BCF/VCF scans pin their parsed indexes; reprepare to use a changed index. Data/header contents must remain unchanged and the initial index must match.

DuckVEP annotation and haplotype replay

• Add rduckhts_haplotypes() for shared CDS/protein paths with complete carrier and contributor evidence, coding blocks, local coding status and aligned CDS/protein differences. Per-call capacities bound native replay, alignment and HGVS storage; exhaustion raises errors. DuckDB input/output memory is outside the native workspace limit.
• Support explicit decoded-call phase policies and input_mode = "source_records" for original GT spelling and complete ALT lists. Preserve missing/unphased, conditional, overwritten and noncoding contributors. Known REF slots remain distinct from selected skipped ALTs. Model/REF failures retain unavailable sequence rather than fabricated output.
• Add hgvs = TRUE for supported protein HGVS with explicit unsupported states and max_hgvs_reference_bytes. Frame restoration does not erase physical edits or downstream contributors; stop_in_displaced_frame is not a protein rescue prediction. nominal_length_diff differs from rebuilt CDS length when source replacement clipping changes the applied span.
• Correct bundled SNV/MNV/indel consequences and protein HGVS around phase-padded CDS starts, partial terminal codons, UTR/CDS transitions and transcript ends. N-containing codons use pinned VEP-116 consensus where defined; literal REF validation and unavailable-context states remain explicit.
• Match VEP-116 transcript HGVS for literal SNPs whose CDS begins after a noncoding exon, clipped coordinate ordering and reverse-strand insertions shifted immediately outside transcript start. Returned HGVS columns are accession-free bodies; model metadata supplies serialized identifiers.
• Expose bundled duckvep_transcript_projection(), duckvep_breakend_geometry() and duckvep_repeat_alleles() through SQL/DBI. These provide typed transcript display, raw BND preparation and bounded paired exact-repeat preparation. Correct the paired-BND truncation/intergenic union. BND replacement text is not inserted-only sequence; repeat summaries do not establish an exact allele. Transcript display shares decoded reference sequences and extracts local codon spans to reduce per-event memory use.
• Handle empty known regions, invalid/short CDS models and all-NULL phase lists safely. Nested/concurrent model or haplotype preparation returns a busy error; completed scans retain independent state.

Haplotype replay remains alpha: local coding facts and supported protein HGVS are not complete whole-haplotype SO/IMPACT/NMD, compound DNA HGVS, structural composition or altered-splicing prediction. Strict phase policy does not select a different HGVS nomenclature standard. Pinned Ensembl VEP 116 is the compatibility target, with unresolved cases and policy differences preserved. Circular annotation and mapped MANE-on-GRCh37 enrichment are not provided.

Reader safety and reference handling

• Retain no-coordinate BAM/CRAM reads exactly once in automatic full-file scans, including older indexes without tail counts. Read/iterator and reader-state allocation failures return recoverable DBI errors instead of partial output.
• Reject empty region-list items and malformed known-contig intervals. NULL/empty-string selection still means no filter; repeated FASTA requests retain repeated rows and literal comma/colon contig names.
• Return BAM FILE_OFFSET only for BGZF BAM, as the virtual position after each record. SAM, CRAM and uncompressed BAM return missing values; use explicit SQL ordering when required.
• Report BAM CIGAR/AUX/SAMPLE_ID, INFO/FORMAT/GT and list-allocation failures without fabricated missing fields, lost buffers or unusable connections. Decoded-capacity overflow is distinct from out-of-memory failure.
• Keep normalization/munging reference caches thread-owned and bounded to eight handles and eight 64-KiB windows per thread, preserving aliases and per-call remote-I/O settings. rduckhts_fasta_nuc() reports reference-fetch errors instead of omitting intervals.
• Bound bundled liftover clip-pad alignment to 4,194,304 cells and return recoverable errors for malformed bundled bcftools score filters.

Installation, compatibility and migration

• Provide concise function summaries and a bundled SQL reference with signatures, return schemas, usage contracts and examples, linked from the package README.
• Quote wrapper paths/options through DBI literals and object names through DBI identifiers, while preserving explicitly documented SQL-expression arguments.
• Compile a registered R native library so binary repositories record the actual target architecture. Binary publication checks the package Built field against the bundled extension metadata.
• Keep live-database rejection tests independent of DuckDB error wording, checking connection/driver validity and unchanged unsigned-extension policy across the tested released and upcoming DuckDB R versions.
• Remove experimental bundled read_bcf_v2 and read_bcf_appender. Use read_bcf() or supported R wrappers with projection, explicit sequential mode where needed, and DuckDB CTAS/INSERT/COPY for materialization. Experimental-only arguments are not transferred.
• Remove the unsupported duckhts_build() manual compiler. Package configure scripts own compilation; maintainer dependency installation is explicit.
• Custom DuckVEP model queries use the 13-column complete-flank or 11-column CDS-only form. The 12-column short-tail form and post_cds_bases are removed. Alpha coding blocks use event_indices for physical-edit provenance, replacing the count-only field.

Rduckhts 1.5.1-0.1.4

• declare NeedsCompilation: yes because package configuration compiles target-specific DuckHTS and htslib artifacts outside the conventional R src/ directory. Binary repositories can no longer treat an x86_64 package as architecture-independent and reuse it on Linux ARM64. Native Linux ARM64 coverage now builds and audits a clean source tarball, installs it, loads the linux_arm64 extension, and validates the bundled htslib receipt

Rduckhts 1.5.1-0.1.3

• derive the Windows DuckDB extension platform from R’s target and require the compiler target to agree, instead of trusting the architecture reported by the MSYS shell. Native Windows ARM64 package coverage now builds a clean source tarball, installs it, loads the windows_arm64_mingw extension, and validates the bundled htslib receipt
• preserve R and site compiler-warning policy during released package installs instead of promoting every externally enabled warning to an error. Strict package-owned diagnostics remain an explicit CI gate, vendored htslib headers are system includes in Unix-like package builds, and the macOS package check reproduces CRAN M1Mac’s conversion-warning flags
• add rduckhts_connect() as the single package-owned connection path. It explicitly permits the locally compiled bundled extension, uses temporary DuckDB extension/secret storage when supported, and disables implicit known- extension installation and loading. Package examples and extension-dependent tinytests now use this path, including on CRAN’s Linux libc++ builds where the duckdb package otherwise disables extension loading. duckhts_load(NULL) delegates to the same connection contract, while rduckhts_load() remains available for caller-owned connections. File-backed connections reject a reused DuckDB driver, whose creation policy cannot be changed, and release a newly owned driver if connection or extension loading fails

Rduckhts 1.5.1-0.1.0

• make bundled-extension compilation promote DuckHTS and libBigWig diagnostics to errors by default, including CRAN-like Fedora Clang builds
• bundle the bcftools_norm_row out-of-memory cleanup correction so a failed internal allocation cannot use an indeterminate allele-buffer count
• bundle the libBigWig strict-prototype correction so macOS Clang package installation no longer warns about the bwCleanup definition
• bundle VEP-116-compatible gVCF event dispatch: expanded <NON_REF>, bare *, and . ALT rows produce no annotations; literal ALTs from mixed records remain small variants; and <*> produces the generic coding or retained start/stop consequence with empty HGVS. Record-level INFO/END remains provenance for literal ALTs and <*>. The package docs and tests also warn that VEP 116’s literal allele-length handling can emit an ablation term when a long-REF <*> row completely contains a feature
• remove the DuckHTS-source diagnostics reported by the Debian and Windows win-builder package pretests, including the MinGW hidden-visibility warnings
• link the package DuckVEP documentation to the illustrated whole-genome DuckVEP/FastVEP speed, memory, VEP-conformance, fastSA-versus-SQL provider, algorithm-design, and test-infrastructure report
• make the in-memory downstream htslib consumer test compatible with both the original and argument-capable Rtinycc::tcc_call_symbol() APIs, and bundle bounds-checked BAQ tag renaming so GCC 11 package builds do not emit the former zero-size-region warning
• clarify the bundled DuckVEP catalog and README: the resident kernel is transcript-source-neutral, the package builder currently compiles the Ensembl core set, and transcript-to-genome sequence corrections, circular-origin geometry, implicit path projection, and phased composition remain outside the package surface
• make the Fedora CRAN-reproduction flow install the suggested Rtinycc downstream-linking test dependency before strict package checks
• clarify in the bundled DuckVEP function catalog that the supplied reference defines the exact modeled sequence paths and that annotation does not implicitly project X/Y PAR, patch, or alternate-haplotype coordinates. Package documentation now distinguishes official Ensembl Variation release-VCF product audits from executable-VEP compatibility
• bundle the VEP-116 protein-HGVS endpoint fix: a coding insertion that copies the final translated residue no longer becomes a protein duplication when VEP’s post-variant peptide lookup would suppress the 3-prime shift
• bundle duckvep_allele_geometry(...), which returns the raw VCF span, VEP feature span, minimized edit span, and insertion point used by the consequence engine. The bundled cumulative consequence/HGVS path now reuses one projected transcript edit and one coding fact object per event/transcript pair, with release-specific VEP-116 HGVS behavior selected through a named compatibility policy rather than formatter-local constants. Add DBI coverage for the geometry contract and regenerate the package function catalog
• make the bundled duckhts_bcftools_norm(...) derived-query macro accept the VARCHAR[] ALT column returned by read_bcf(). The scalar and list forms of duckhts_alt_to_list(...) and bcftools_norm_row(...) are now registered as DuckDB overload sets, matching the package’s documented normalization workflow
• bundle peak-capacity preflight for exact-alias multi-edit CDS application. A length-neutral edit set whose first applied insertion temporarily grows the CDS now returns BUFFER_TOO_SMALL before changing the caller buffer when that intermediate sequence exceeds its capacity
• add rduckhts_htslib_config() as the versioned installed-package contract for downstream C/C++ packages linking to the bundled htslib. It resolves exact headers, shared/static libraries, static dependencies, loader flags, plugins and compiled features from the installed package, and rejects receipt/header/runtime version disagreement through the extension-owned htslib diagnostics. Add thin rduckhts_htslib_info() and rduckhts_htslib_version() helpers plus an in-memory downstream compile/link test, built through Rtinycc with active-SDK system headers on macOS, that opens bundled BAM, CRAM, BCF, and VCF files. When link is omitted, select the shared or static contract chosen during package configuration. The compatibility htslib_rpath() helper follows that configured contract, so static-only installations return an empty loader path instead of validating a missing shared library
• bundle the projection-aware read_bigwig(...) table function and rduckhts_bigwig() materialization/view helper. Region vectors use htslib’s one-based inclusive syntax while returned intervals retain stored zero-based, half-open coordinates. Add the pinned upstream libBigWig fixture, DBI tests, package examples, Devon Ryan’s copyright-holder attribution, and the vendored MIT license. Oversized chromosome tables, malformed chromosome-tree IDs, truncated zoom headers, unreadable R-tree indexes, oversized block allocations, and truncated data blocks return reader errors before indexed storage or interval decoding
• reorganize the rendered package DuckVEP example into explicit design/validation, supported-scope, current-gap, and executable-example sections. The documentation now distinguishes independent-event consequence/HGVS support from combined haplotypes, imprecise-SV/STR policy, and supplementary provider relations
• bundle VEP-116 compatibility fixes for complete first-codon in-frame deletions on transcripts without a 5-prime UTR and for pure insertions in incomplete terminal codons. The latter can now return the exact VEP combination incomplete_terminal_codon_variant&inframe_insertion&stop_gained together with c.280_281insAGT and the apparently contradictory p.Ter94= protein rendering. A bundled DBI regression exercises both rare states through the public duckvep_annotate(..., rich = TRUE, hgvs = TRUE) relation; its terminal-codon case uses an exact remapped GRCh38 transcript/reference fixture with enough downstream sequence to pin the one-base VEP 3-prime shift
• make bundled mitochondrial HGVSp reproduce VEP 116’s late termination search, which uses the standard codon table even when ordinary transcript translation uses mitochondrial table 2, and render a combined frame-changing terminal deletion plus cached stop loss through VEP’s deletion-extension precedence
• bundle rare HGVS compatibility fixes. Shifted in-frame start-loss insertions perform VEP’s sequence-dependent peptide-level 3-prime rotation; position-1 shifted frameshifts retain Ter?, while later frameshifts can repeat VEP’s late original-coordinate, original-allele stop search; and terminal complete-feature clamping can render a duplicated transcript base even when minimization moved the differing base outside the transcript. Bundled SQL behavior is pinned by exact HGVSc/HGVSp witnesses
• bundle duckvep_annotate(..., rich := TRUE) so DBI workflows can request VEP-facing consequence, IMPACT, region, amino-acid, NMD, overlap-object, and explicit DuckHTS audit text without losing the compact numeric fields. rich := TRUE, hgvs := TRUE returns those fields and independent-event HGVS from one fused native pass. Add DBI coverage for the public rich/HGVS schema and regenerate the package function catalog from the public SQL authority
• make the bundled duckvep_annotate(...) relation reject conflicting supported symbolic ALT and explicit structural-type values, and treat explicit hgvs := NULL as the documented FALSE default instead of filtering small variants from both annotation lanes
• bundle the unified duckvep_annotate(events_table, model_name, hgvs := false, ...) relation and generated duckvep_so_terms() lookup. DBI callers can keep one narrow mixed small/SV/BND event table, request independent-event HGVS without changing schemas, decode consequence masks after filtering, and join selected rows back by event identity. Add a bundled public-surface tinytest and a deterministic model-to-annotation example in the rendered package README
• bundle duckhts_contig_key(...) for DBI workflows that need a conservative join key across chr-prefixed VCF/dbSNP contigs and Ensembl-style region names. The helper normalizes mitochondrial M/MT to MT and uppercase X/Y but deliberately does not guess numeric sex chromosomes, accessions, patches, or alternate loci
• reset bundled DuckVEP exon cursors before a worker workspace is reused after a non-monotone normalized-event vector, preventing a transcript skipped after a forward jump from carrying an ahead exon rank into the next DBI vector
• fix bundled cumulative HGVS output for strings larger than the native renderer’s initial scratch capacity. The bundled adapter retries with the reported exact capacity instead of exposing truncated text, retains a failed UTF-8 assignment as NULL, and rejects an invalid internal text slice. A DBI regression exercises a transcript HGVS string longer than 1,400 bytes and an independently rendered protein HGVS string beyond the initial capacity. Cumulative annotation preserves resident regulatory/motif rows from the same pass with NULL HGVS fields, so DBI callers do not need a second annotation scan
• speed up the bundled DuckVEP consequence and cumulative HGVS paths by reusing one classification pass and compact prepared facts. Bundled annotation now preserves deterministic annotation_index values across DuckDB vector and disjoint ordered partition starts. The resident model remains immutable and shared. Tests also cover zero-, 10,000-, and 50,000-base transcript distances so the bundled behavior is not specialized to the default distance
• bundle duckvep_annotate_hgvs(...) for DBI workflows that need compact independent-event consequence rows together with transcript c./n. and default-VEP protein p. HGVS suffixes, the applied 3-prime shift, and explicit supported/unresolved/not-applicable states. Bundled duckvep_model_load(...) can bind an existing indexed reference FASTA through an exact ordinal/name/length relation; it does not create an index and retains open read descriptors for the validated FASTA, .fai, and optional .gzi. Linux workers reopen those descriptors, Windows keeps a resolved source under deny-write sharing, and other POSIX workers use independent resolved-source handles with identity checks rather than sharing /dev/fd seek state. Annotation workers own separate faidx handles, reuse contained sorted reference windows, and reject detectable in-place source mutation around a fetch. Explicit NULL optional model queries and reference parameters behave like omission. Bundled tests cover reference-backed substitution and insertion rendering through the public DBI surface. Transcript rows admitted only by an upstream/downstream distance report HGVS not_applicable, matching VEP’s absent HGVSc, rather than an unresolved projection. Literal exonic SNP HGVSc also retains VEP 116’s phase-aware CDS-start fast path without shifting intronic SNP, indel, or multi-base feature coordinates. Protein HGVS reports not_applicable when the VEP feature has a leading or trailing genomic-to-peptide mapper Gap. Reference failures use VEP’s cached complete-feature coding predicate, so a 5-prime-UTR insertion that could shift into CDS remains protein-unresolved rather than falsely not applicable. A bundled model without FASTA now reports missing_reference when retained uploaded REF padding or an anchor cannot be checked by the prepared CDS, instead of validating only the minimized differing REF. The bundled reference path keeps VEP’s exact +/-1000 shift slice separate from complete uploaded-REF validation and adjacent duplication-source lookup, so retained padding does not change the shift and copied sources longer than 1000 bases still render as dup. Endpoint-overlapping transcript edits retain VEP’s clipped transcript-slice coordinates, and protein replay reproduces VEP’s one/two-base alternate-CDS trimming assignment bug before appending the 3-prime UTR. Bundled HGVS execution now reuses the kernel-prepared model, derives each reference first stop once, defers CDS projection until protein HGVS needs it, scans a virtual single-edit CDS instead of rebuilding the complete alternate sequence, and renders through a reusable worker buffer. The bundled consequence sidecar shortcut remains fail-closed for length-changing splice overlaps: without a positive frameshift fact, those edits run the complete peptide delta so their VEP-compatible frameshift HGVSp is retained
• bundled DuckVEP now gives ordinary long literal deletions the same complete- transcript transcript_ablation semantics as symbolic deletions. Equal-length containing alleles also preserve VEP 116’s otherwise-empty endpoint UTR terms without leaking an internal unknown-coding fact into coding_sequence_variant; bundled DBI tests pin both public results
• speed up bundled paired-BND annotation by preserving the already sorted transcript stream and linearly merging only the much smaller resident regulation-feature stream; transcript-only models no longer sort the full expanded result before returning one list per input event
• bundled paired-BND annotation now keeps VEP’s fixed 5000-base overlap-allele admission independent of a caller-selected zero transcript window: an admitted local allele whose directional predicate is disabled contributes default intergenic_variant beside mate-derived feature_truncation. Add bundled DBI regressions at zero and wider caller distances
• bundled DuckVEP exact structural annotation now accepts STR/TANDEM_REPEAT/CNV:TR spans and preserves structural tandem-repeat identity while matching VEP 116’s tandem-duplication consequence predicates. Bundled paired-BND annotation now returns RegulatoryFeature and MotifFeature rows found at either endpoint, once per feature, in addition to transcript consequences; local exact hits keep the base object term, mate-only exact hits use VEP’s generic HIGH-impact feature_truncation, and a shifted local point on the same contig but outside and within 5000 bases adds intergenic_variant to that mate-discovered object. The local base term wins when both points hit one object exactly, and mixed transcript/regulation batches preserve one result list per input event. A caller-selected transcript distance above 5000 does not widen VEP’s separate fixed structural-breakend allele-admission cap. Add DBI tinytests for these surfaces and update generated function documentation Structural adapters consume nominal POS/END geometry, matching VEP 116’s registered consequence predicates; callers retain CIPOS/CIEND, inserted sequence, and raw repeat metadata beside the result for provenance, later HGVS, and round-trip rendering
• fix bundled projected read_fastq(...) scans so FASTQ headers longer than the BAM query-name limit remain usable when NAME / PAIR_ID are not requested and no paired-file comparison needs them; name-producing scans retain the htslib-compatible limit. An explicit bundled duckhts_fastq_qc(..., max_cycles) value below 128 now also caps the initial per-group cycle allocation
• bundle duckhts_fastq_qc(sequence, quality [, max_cycles]) for DBI workflows that need exact global and per-cycle FASTQ quality statistics without expanding one row per base; the bundled scalar, AVX2, ARM NEON, and wasm SIMD128 implementations share one dispatch contract, and tinytests compare forced scalar with automatic selection over grouped and malformed inputs
• accelerate bundled read_fastq(...) scans by parsing FASTQ directly over htslib transport into projected DBI columns instead of round-tripping through temporary BAM records; multiline records, htslib-style query names, paired/interleaved checks, string and packed nt16/Phred output, quality conversion, and count behavior are retained, while truncated quality blocks now surface as R/DBI errors. Add bundled multiline, packed-output, and truncation tinytests
• fix duckhts_build(...) to obtain the DuckVEP kernel source list from the package’s shared source-list helper; the fallback no longer references a variable local to duckhts_bootstrap(...)
• bundle htslib 1.24 and use its native deduplicating BCF/tabix multi-region iterators in the DBI-visible indexed readers. Repeated or overlapping regions passed to bundled read_bcf(...), read_bcf_v2(...), read_gff(...), read_gtf(...), read_tabix(...), and read_bcf_appender(...) calls now return each matching record once. The appender partitions region_threads work by primary contig while retaining one native iterator for that contig’s complete interval set, so thread count no longer changes its target schema or row multiset; remove the thread-only duckhts_region_idx column and retain opt-in FILE_OFFSET for restoring file order. Bundled read_bam(...) already uses the equivalent deduplicating alignment iterator. Keep BCF work claiming iterative and bounded to 16 workers, with bundled regressions over 256 leading header-only contigs and empty requested contigs. Build htslib as GNU C17 so GCC 16 does not apply its GNU C23 default to this pre-C23 dependency. Add bundled tinytests and a Fedora GCC 16 R-devel package check matching CRAN’s Fedora compiler environment
• bundle release-matched Ensembl RegulatoryFeature and MotifFeature preparation and integrated consequence output for DBI workflows. duckvep_model_load(...) accepts the compact feature projection, while duckvep_annotate(...), its compact form, and exact structural adapters return typed transcript or regulation/motif rows from one call; cold funcgen metadata remains joinable by feature ordinal. The existing eight-argument model-receipt call remains valid and accepts regulation_features_table as an optional named relation. Bundled model receipts validate, count, and hash feature geometry, exclude the same EMAR rows as VEP 116, and the offline fixture includes exact core/funcgen provenance plus three real MotifFeature rows on KI270395.1
• bundle dedicated duckvep_annotate_breakend(...) and duckvep_annotate_breakend_compact(...) functions. DBI callers provide both raw VCF loci in one row and retain raw ALT, bracket orientation, event identity, and provenance as ordinary columns; the bundled engine queries transcripts around both endpoints and returns the VEP-116 consequence-set union once per transcript. Mate-only consequences have NULL rich region / zero compact region mask
• bundle typed exact structural-span consequence functions duckvep_annotate_sv(...) and duckvep_annotate_sv_compact(...); DBI callers provide one-based inclusive spans for DEL/DUP/TDUP/INV/CNV/UNKNOWN, or start = end = P for an INS after reference base P, plus explicit copy direction. Contradictory metadata fails as an error. The bundled consequence mask retains stable assignments for all 41 terms in VEP 116’s registry, including regulatory-region and transcription-factor-binding-site terms
• bundled DuckVEP now matches the pinned VEP Plugins release/116 NMD implementation’s separate feature geometry: consequence and sequence changes use the minimized edit, while NMD CDS and exon-end rules use the complete VEP feature. This fixes padded equal-length alleles crossing an early-CDS or penultimate-exon threshold and insertions at coding exon edges, whose parent VEP object keeps a reversed CDS range—including the defined 1,0 range immediately before CDS base 1; the cached first-101-CDS-base result is reused only when both spans are identical
• bundled DuckVEP now reuses resolved intron coordinates while evaluating non-SNV mismatch islands and skips predicate evaluation when no intron, splice, or short-intron fact can change; the sorted-SNV classifier remains inlined
• bundled DuckVEP now prepares validated CDS-to-cDNA projection coordinates once per resident transcript, avoiding repeated CDS-endpoint searches while annotating coding variants; topology-only transcripts retain the existing exhaustive projection behavior, and the common sorted-SNV lane keeps a stable instruction-cache-aligned entry
• bundled DuckVEP now rebuilds multi-edit CDS haplotypes in one linear reverse-coordinate pass over distinct reference and worker-scratch buffers, replacing one CDS-tail move per edit while preserving edit, strand, reference-validation, and exact-alias behavior
• bundled duckvep_annotate(...) and duckvep_annotate_compact(...) now accept VEP-style separate upstream and downstream distances in addition to the existing shared distance; omitted values retain the 5,000-base default and zero disables that direction
• bundled DuckVEP now reproduces VEP 116’s reverse-strand insertion-length terminal-stop fallback, reconstructing the original CDS endpoint after the edit before deciding whether the terminal stop is retained
• bundled DuckVEP now reproduces VEP 116’s independent unknown-coding and missense predicates for equal-length edits on incomplete-start transcripts
• bundled DuckVEP now matches VEP 116 for an insertion after the final base of a mature-miRNA segment: VEP’s minimized reversed insertion interval does not overlap that segment, so annotation returns non_coding_transcript_exon_variant instead of a false mature_miRNA_variant; the regression covers both transcript strands
• bundled DuckVEP model preparation now reads Ensembl sequence-region codon-table attributes and supports the full VEP 116/BioPerl codon-table set. Valid single-residue initial-methionine, selenocysteine, curated amino-acid-substitution, and stop-readthrough edits can be packed by duckvep_model_load(...) and are applied to the reference peptide during annotation; unsupported edit shapes remain fail-closed. Numeric-only attribute columns inferred as integers by dump staging are accepted at the importer boundary. Model receipts hash and count mature-miRNA segments and peptide edits, and the bundled GRCh38 and GRCh37 fixtures exercise real mitochondrial codon-table and peptide-edit behavior
• duckvep_ensembl_transcripts(...) now applies VEP’s core-transcript selection and projects mature-miRNA cDNA attributes into genomic exon segments; duckvep_model_load(...) accepts those segments through optional mature_mirna_query, and annotation returns mature_miRNA_variant with VEP’s precedence over generic non-coding exon terms. The bundled engine also fixes insertion placement at transcript/exon edges, VEP’s empty-UTR endpoint behavior, and coding edits on CDS_END_NF transcripts with a one- or two-base partial terminal codon; DBI tests cover the complete Ensembl-import-to-resident-model path
• bundle duckvep_annotate_compact(...), returning the same DuckVEP transcript consequences as numeric SO/region masks and stable status, reason, amino-acid, and NMD codes so DBI workflows can filter and join before rendering strings. The bundled rich annotation path also caches DuckDB vector validity and string lengths per chunk; SQL and tinytests check numeric-code semantics and parity with duckvep_annotate(...)
• bundled DuckVEP now uses one edit/CDS/peptide context for length-changing small variants instead of retrying failed contexts through a shape-specific classifier. Complete transcript-oriented sequence before and after the CDS supports VEP 116’s independent start/stop predicates, endpoint-mapper-Gap behavior, and transcript-associated default intergenic_variant; duckvep_model_load(...) accepts the complete 13-column projection while retaining its 11/12-column compatibility, and older models return missing_transcript_flank rather than guessing
• bundled duckvep_annotate(...) now matches VEP 116 for equal-length features crossing from 5-prime UTR into the start codon: changing the start returns start_lost without a co-occurring stop term, while preserving ATG returns start_retained_variant even when later coding bases in the same uploaded feature change; DBI regressions pin each state
• bundled duckvep_annotate(...) now matches VEP 116 when unchanged bases retained in an equal-length uploaded feature widen the peptide-predicate window beyond the trimmed sequence edit, including representation-dependent start_lost&start_retained_variant, stop_retained_variant, missense_variant, and stop_gained results pinned by paired DBI regressions; retained REF mismatches and ambiguous widened windows now return explicit unresolved reasons instead of retrying the smaller edit
• bundled DuckVEP annotation now matches VEP 116 when an equal-length uploaded feature crosses from CDS into the transcript-oriented 3-prime UTR: it preserves VEP’s unavailable peptide-mapping state and returns coding_sequence_variant rather than a stop or missense consequence derived from a smaller trimmed edit
• make bundled duckvep_annotate(...) reproduce VEP 116 when ALT-only mismatch bases extend from an exonic REF-shaped feature into an intron, including VEP’s three-base interval-tree cache boundary and co-emission with coding and splice terms
• make bundled duckvep_annotate(...) classify length-changing coding edits from VEP 116’s codon-local predicate inputs rather than whole-protein or net-length shortcuts. This fixes stop-gained insertions whose preserved peptide flank lies after the new stop, and delins that change length by a complete codon but are protein_altering_variant rather than in-frame insertion/deletion
• make the bundled duckvep_annotate(...) match VEP 116’s terminal-stop insertion predicate order, including non-modulo-three insertions that VEP reports as inframe_insertion together with coding_sequence_variant, stop_lost, or stop_retained_variant; unsupported contexts remain explicit
• bundled duckvep_annotate(...) now keeps uploaded VCF geometry, VEP parser feature geometry, and the semantic sequence edit distinct, fixing candidate, splice, start-codon, and terminal-stop consequences for padded and multi-base alleles
• bundled duckvep_annotate(...) now predicts whether eligible stop-gained, frameshift, splice-donor, and splice-acceptor consequences trigger or escape nonsense-mediated decay under the pinned VEP Plugins release/116 policy, with separate boolean escape reasons and explicit unresolved state when coding placement is unavailable. This remains distinct from NMD_transcript_variant, which identifies an already curated nonsense-mediated-decay transcript biotype
• bundled read_bcf() and read_bcf_v2() now recognize the Format=... CSQ schema spelling in Ensembl variation release VCFs and expose typed VEP_* columns through DBI queries
• retain versioned RefSeq accessions from MANE Select and MANE Plus Clinical in bundled prepared transcript relations while keeping the resident model compact; reject empty or conflicting MANE mappings. Fix bundled duckvep_model_receipt(...) provenance column names and add roughly 116 KiB of offline Ensembl-116 GRCh38 and GRCh37/GENCODE-19 fixtures to package tests, covering real MANE, ordinary coding, and mitochondrial missing-sequence behavior without network access during CRAN builds or checks
• bundle duckvep_ensembl_regions(...), duckvep_ensembl_transcripts(...), and duckvep_model_receipt(...), allowing DBI workflows to prepare a validated, provenance-hashed resident DuckVEP model directly from Ensembl core relations and matching tiled FASTA sequence. Unsupported Ensembl RNA/peptide edits keep their model flags but return explicit missing-sequence state instead of ordinary coding predictions, including _rna_edit records carried by either transcript or translation attributes; bundled SQL and tinytests cover both strands, nested exon projection, receipt generation, and resident loading
• accept Ensembl exon phase -1 in bundled sequence-backed models when translation begins after 5-prime UTR within that exon, matching VEP’s zero-prefix interpretation while retaining exact prepared-CDS validation
• bundled DuckVEP annotation now follows VEP 116 for frame-changing edits that begin in the terminal stop, returning stop_lost or stop_retained_variant instead of a false frameshift. The resident transcript query accepts an optional twelfth post_cds_bases BLOB with up to three transcript-oriented bases; when a terminal deletion needs absent tail sequence, the result is explicitly unresolved as missing_transcript_tail
• bundled DuckVEP annotation now matches VEP 116 for insertions at exon, CDS, and transcript boundaries, including coding+splice consequences when the VCF padding base is intronic and UTR/downstream placement at right-hand boundaries
• expose specific DuckVEP unresolved reasons through the bundled extension and return NULL, rather than empty strings, when a protein-positioned frameshift or in-frame indel has no scalar one-letter amino-acid value
• reject malformed bundled DuckVEP resident models at load time when transcript/exon/cDNA/CDS/phase/prepared-sequence coordinates disagree; the SQL loader and standalone C engine now share the same final validator
• make bundled DuckVEP intergenic output fail closed for partial resident models. Ordinary duckvep_model_load(...) calls report no_feature_in_loaded_model as unresolved; the named transcript_coverage_complete := TRUE parameter requires contig lengths before returning supported intergenic_variant, and rejects coordinates beyond those lengths
• fix bundled duckvep_annotate(...) handling of padded small variants: whole-allele padding no longer turns a one-base substitution into an MNV, and VCF position-1 insertions/deletions with a following padding base are accepted
• speed up the bundled DuckVEP engine for coordinate-sorted SNVs by retaining compact per-transcript exon cursors across adjacent DuckDB chunks and by avoiding full Sequence Ontology scans for the common single-consequence rows; this does not change the existing MNV/indel/SV span classifiers or grouped-haplotype edit core
• bundled DuckVEP annotation now emits VEP-116 NMD_transcript_variant for variants inside transcripts imported with the nonsense_mediated_decay biotype
• bundle the DuckVEP SQL surface: duckvep_model_load(...) loads and validates one of several named resident transcript models from committed DuckDB relations, duckvep_annotate(...) returns explicit per-transcript consequence rows for biallelic small variants, and duckvep_model_drop(...) releases a model. Add an end-to-end DBI tinytest using the bundled extension and a sequence-backed coding transcript

Rduckhts 1.4.0-0.1.0 (2026-07-10)

• accelerate the bundled bam_nt16_counts and nt16_gc_counts logical kernels on AArch64 with NEON, so Apple Silicon and other arm64 package builds no longer fall back to scalar for BAM-bin GC counting or nt16 seq_gc_content(...); add conditional tinytests that require every reported complete backend to own all three sequence-kernel slots and match scalar results. Emscripten package builds now keep bam_bin_counts(...) on its synchronous no-index path by disabling unavailable htslib worker threads
• bundled cigar_* helpers (cigar_has_soft_clip, cigar_has_hard_clip, cigar_left_soft_clip, cigar_right_soft_clip, cigar_query_length, cigar_aligned_query_length, cigar_reference_length, cigar_has_op) are overloaded to accept a UINTEGER[] binary CIGAR from read_bam(cigar_representation = 'binary'), and bundled seq_hash_2bit(...) is overloaded to accept a UTINYINT[] of htslib nt16 codes from read_bam(sequence_encoding = 'nt16'). Both are bit-identical to the text path, so DBI pipelines analyze the projection-pushed binary columns without decoding to text; add bundled tinytest coverage
• bundled rduckhts_simd_kernel_info() now reports an additional nt16_gc_counts logical kernel, and the bundled nt16 seq_gc_content(...) overload is routed through the SIMD dispatch framework; GC results are unchanged (a scalar reference backend is the correctness oracle), and forced scalar vs auto agree (bundled tinytest coverage added)
• bundled seq_revcomp(...) and seq_canonical(...) are overloaded to accept BAM nt16 sequences: in addition to text they take the UTINYINT[] of htslib nt16 codes from read_bam(sequence_encoding = 'nt16') and return UTINYINT[], so DBI pipelines can reverse-complement and canonicalize directly on the nt16 column. Non-ACGTN codes yield NULL as in the text path; results are bit-identical to the text path after decoding; add bundled tinytest coverage
• bundled seq_gc_content(...) is overloaded to accept BAM nt16 sequences: in addition to a text sequence it now takes the UTINYINT[] of htslib nt16 codes returned by read_bam(sequence_encoding = 'nt16'), so DBI pipelines can compute GC directly on the projection-pushed BAM column without decoding to text. The nt16 result is bit-identical to the text path; add bundled tinytest coverage
• bundled read_bcf(...), read_bcf_v2(...), and read_bcf_appender(...) gain decode_error_policy := 'null'|'warn'|'error' for corrupt BCF FORMAT/INFO header-vs-payload type clashes; the default null policy materializes NULLs, warn emits a DuckHTS warning and materializes NULLs, and error raises a DuckDB/R error. FORMAT and INFO decode now preflight under every policy (including the default null), so corrupt inputs neither trigger htslib exit(1) termination nor leak raw bytes; an INFO field whose header claims Type=String over a numeric payload previously returned truncated garbage under the default policy and now materializes NULL. Add bundled corrupt-BCF fixtures (including a reverse String-header/numeric-payload clash) plus tinytest coverage while keeping valid mixed-ploidy Number=G FORMAT records accepted
• bundled rduckhts_simd_kernel_info() now reports an additional bam_nt16_counts logical kernel, and bundled bam_bin_counts(...) GC base counting is routed through the SIMD dispatch framework; GC results are unchanged (a scalar reference backend is the correctness oracle)
• surface malformed-record BCF/VCF scan failures from bundled read_bcf(...), projected read_bcf_v2(...) scans, and non-parallel read_bcf_appender(...) as DuckDB/R errors instead of treating htslib parse/read failures as EOF; run bundled read_bcf_appender(...) writes in an internal transaction so malformed input rolls back target-table side effects; add a malformed-POS fixture plus tinytest coverage
• bundle the restored experimental read_bcf_v2(...) table function for DBI users, preserving read_bcf(...) schema compatibility while adding sample pushdown, INFO/FORMAT/VEP field filters, projection-aware VCF unpacking, persistent decode caches, and count-only shortcuts for benchmarking
• bundle the initial experimental read_bcf_appender(...) benchmark helper for DBI users; at introduction, its single-stream path was transactional while the region_threads > 1 path was explicitly best-effort and lacked rollback (the current development entry above records its later transactional, thread-invariant contract)
• bundle the experimental hts_region_union_query(...) scalar macro for DBI users, which generates a UNION ALL BY NAME query string reading one HTS file through separate per-region scans; the generated query does not deduplicate boundary-spanning records
• fix bundled read_bcf_appender(...) so a region query matching no records still creates and commits the empty target table instead of rolling back its DROP/CREATE TABLE, which previously could leave a stale prior table under overwrite := true or never create the target
• add bundled tinytest coverage for malformed additional_csq_column_types so invalid CSQ/ANN/BCSQ type override rules fail as DuckDB/R errors instead of proceeding with ambiguous parsed-annotation typing
• update the bundled DuckDB C API headers to DuckDB v1.5.3 while keeping stable extension ABI metadata at v1.2.0; bundled SQL sessions loaded through rduckhts_load() now expose DuckDB runtime type-support probes for VARIANT and GEOMETRY
• simplify the bundled rduckhts_bcftools_norm() / duckhts_bcftools_norm(...) site-preserving table-macro query shape by removing the extra correlated scalar LATERAL subquery around bcftools_norm_row(...), eliminating the site-preserving LEFT_DELIM_JOIN plan overhead while preserving split-mode ALT row semantics and caller columns whose names collide with DuckHTS helper-column names used internally by earlier macro forms; add tinytest coverage for DuckDB’s suffixed behavior when callers already have normalized-output column names
• expose bundled reader scan_mode = "auto"|"sequential" controls through the R wrappers and multi-file helpers for read_bcf, read_bam, read_fasta, read_fastq, read_bed, read_gff, read_gtf, and read_tabix, so callers can force full-file streaming/counting instead of index-backed count or parallel scan paths where applicable; sequential mode is rejected for region queries
• optimize bundled bcftools_norm_row(...) / rduckhts_bcftools_norm() for already-normalized plain ACGTN allele rows by skipping kstring left-realignment setup when trim predicates prove the row is unchanged; avoid per-row FASTA path duplication after the vector-local cache is established, reuse larger bounded per-thread reference windows, and document/defensively serialize htslib FASTA fetches while keeping normalization reference caches thread-local to avoid the faidx cache race class fixed in https://github.com/RGenomicsETL/duckhts/issues/17 / https://github.com/RGenomicsETL/duckhts/pull/18
• make bundled rduckhts_bcftools_norm() / duckhts_bcftools_norm(...) gVCF-aware for vt/vcfnorm-style row normalization: <NON_REF> and <*> reference-block alleles now pass through with GVCFReferenceBlock, and mixed real-plus-gVCF-symbolic alleles normalize the real alleles while preserving symbolic alleles and caller-supplied reference-block END in site-preserving output; mixed * plus real alleles now follows the same ignored-symbolic path, while *-only rows remain SpanningDeletion; bundled phased GT/PL/GP/DS/PS FORMAT fixtures, including haploid/triploid/tetraploid Number=G cardinality cases, and tinytests pin phase-separator preservation through read_bcf(...)
• add thin DBI wrappers rduckhts_bcf_convert_parquet(), rduckhts_bam_convert_parquet(), rduckhts_gff_convert_parquet(), and rduckhts_tabix_convert_parquet() around the bundled extension SQL builders duckhts_*_convert_parquet_sql(...); these convert DuckHTS scans to Parquet with DuckHTS write-format metadata, preserved raw headers, optional corrected header text, SQL-filter provenance, selected-column/partition metadata, arbitrary user metadata via R named lists/extension metadata := map(...), optional caller-managed JSON-file metadata when DuckDB’s json extension is available, and partitioned-output support for DuckLake-style registration of premade Parquet files
• include the final VCF #CHROM/sample header line in bundled read_hts_header(..., mode := 'raw'), so Parquet metadata written from VCF/BCF inputs has the complete header needed for future VCF/BCF regeneration

Rduckhts 1.3.0-0.1.0 (2026-05-29)

• expose the rebuilt capability-mask SIMD dispatch diagnostics through rduckhts_simd_kernel_info(), keeping R wrappers thin while reporting one row per logical kernel and preserving backend-agnostic SQL/R conformance tests for seq_gc_content(...)
• harden bundled SIMD backend helpers: retain extension-owned backend-name validation while restoring R-side scalar/non-missing argument shape checks, clarify selectable versus available diagnostics in generated docs, and preserve ASCII SQL quotes for the rendered duckhts_simd_set_backend('auto'|'scalar'|backend) catalog call
• remove htslib autoconf HAVE_* macro guards from all bundled SIMD backend translation units; compile-time gate is now defined(__x86_64__) && (defined(__GNUC__) || defined(__clang__)) for x86 backends, available without autoconf; runtime dispatch and scalar fallback behavior are unchanged; add scalar-vs-auto backend R correctness tests for rduckhts_simd_set_backend() / seq_gc_content(...) covering GC=0/0.5/1.0, embedded-N calling, and soft-masked lowercase bases
• drop internal .validate_simd_backend() R helper from SIMD wrapper functions; backend-name normalization and validation now belong to the extension, while the R wrappers only enforce that backend is a single non-missing character string

Rduckhts 1.2.1-0.1.0 (2026-05-07)

• expose bundled SIMD diagnostics and explicit backend selection through SQL functions and R helpers rduckhts_simd_backend(), rduckhts_simd_requested_backend(), rduckhts_simd_backend_available(), and rduckhts_simd_set_backend(), route bundled seq_gc_content(...) through the new eager scalar/optional-AVX2 runtime dispatch scaffold while preserving scalar fallback behavior on ARM, wasm, and scalar-only builds, add runtime-gated AVX-512, ARM NEON, and wasm SIMD128 backend translation units where compiler-supported, keep the manual duckhts_build() rebuild path wired to the SIMD sources, and add README examples for the scalar/auto SIMD flow
• fix bundled rduckhts_liftover() / bcftools_liftover(...) FASTA contig alias handling during source/destination reference validation and sequence fetches, and align bundled spanning-deletion * allele handling with upstream bcftools +liftover: inputs such as 23, 24, 26, X, Y, MT, and chr* aliases now resolve through the same canonical path, avoiding spurious SourceRefMismatch rejects for X/Y/MT indels when the bundled chain names and FASTA names differ only by canonical aliasing; bundled *-allele rows now follow upstream swap/ref-add semantics instead of taking the symbolic short-circuit path, full-file GIAB conformance against installed bcftools +liftover is now exact, and bundled SQL/tinytest coverage now pins the 23 -> chrX, SWAP=2, and SWAP=-1 regressions
• bundle the official VariantKey / RegionKey C API (Nicola Asuni, 2018; https://doi.org/10.1101/473744) and expose new SQL helpers through rduckhts_load() sessions for both the bcftools-style and raw upstream numeric surfaces: variantkey(...) now matches bcftools %VKX / +add-variantkey on 1-based VCF rows, large/ambiguous/symbolic alleles keep the official hashed nonreversible mode, regionkey(...) adds 0-based half-open span keys plus overlap helpers, bundled tinytests pin reversible and hashed cases, and the package README now includes concrete DBI examples for VariantKey / RegionKey usage
• fix bundled rduckhts_bcftools_norm(..., split_multiallelic = TRUE) row preservation for ref-only and empty-ALT inputs: rows with ALT='.', NULL ALT values, empty ALT lists, or NULL ALT list elements no longer disappear from split-mode DBI results, bundled tinytest coverage now pins the expected RefOnly / NullInput statuses and alt_index behavior, bundled rduckhts_bcf() / rduckhts_bcf_multi() now expose decompression_threads = 0 for explicit htslib worker-thread control on bgzipped VCF/BCF reads, and the package README now includes a concrete normalization example
• fix bundled helper-return metadata for omitted output paths: rduckhts_fasta_index() now returns the generated .fai path when index_path = NULL instead of an empty string, bundled regression coverage now also pins default-path returns for BGZF compression/decompression and BAM/BCF/tabix index builders, and the rduckhts_bgzip() / rduckhts_bgunzip() wrappers now correctly propagate keep = FALSE instead of silently falling back to the extension default keep := TRUE
• add rduckhts_bcftools_norm() and bundle bcftools_norm_row(...) / duckhts_bcftools_norm(...) for bcftools/vt-style FASTA-backed variant normalization from DBI queries: ALT inputs may be either comma-delimited VARCHAR or VARCHAR[], the bundled result appends pos_normed, end_pos_normed, ref_normed, alt_normed, normed, and norm_status, split mode emits one row per ALT with alt_index, and bundled SQL/tinytest coverage now exercises sequence, multiallelic, symbolic <DEL>/<DUP>, and missing-contig rows
• fix bundled rduckhts_liftover() / bcftools_liftover(...) indel parity in two exact upstream rewrite points: repeat-run source extension now keeps extending across the cached source-reference window boundary when needed, and the bundled clip-pad Needleman-Wunsch path now keeps the best shift even when candidate alignment scores are negative instead of leaving padded intervals unshifted; bundled SQL/tinytest coverage now includes dedicated repeat-run and clip-pad regression fixtures, and the real-data conformance workflow reaches exact parity with installed bcftools +liftover on GIAB HG001 chr20 plus the full HG006 GRCh37 benchmark VCF
• fix bundled rduckhts_liftover() / bcftools_liftover(...) row rejection for invalid source-reference indel and difficult-SNP inputs: rows that fail the source-FASTA validation path now stay in the result with mapped = FALSE and reject_reason = 'SourceRefMismatch' instead of fabricating padded lifted alleles or aborting the query; bundled tests and README examples now reflect the reject-row behavior
• add rduckhts_pileup() and bundle native read_pileup(...) for region-scoped BAM pileups with per-position chrom, pos, depth, bases, and quals; expose bundled read_bam(..., cigar_representation := 'binary') through rduckhts_bam(..., cigar_representation = "binary") and multi-file BAM wrappers, returning packed BAM CIGAR ops as UINTEGER[]; and expose explicit gzi_path arguments in rduckhts_fasta(), rduckhts_fasta_multi(), and rduckhts_fasta_nuc() so packaged bgzipped FASTA workflows can use relocated .gzi sidecars
• speed up bundled rduckhts_fasta_nuc() / fasta_nuc(...) nucleotide counting on capable x86_64 hosts with an AVX2+popcnt fast path selected via htslib-style runtime dispatch, while preserving the scalar fallback everywhere else
• improve bundled remote HTS performance for long-running scans and rduckhts_bam_index(): native remote BAM/BCF/tabix/FASTA/BED reads now apply htslib block/cache tuning by access pattern, while wasm/browser builds use the same policy with smaller budgets appropriate for the XHR-backed worker runtime; the bundled vendored htslib also now exposes a pre-opened sam_index_build4(...) entry point so bam_index(...) can be tuned before remote index construction begins
• fix bundled rduckhts_bcf() / read_bcf(...) scanning stability for records where FILTER lists were emitted without reserving list-vector capacity, which could crash with allocator corruption (double free/invalid pointer) during full-table reads; FILTER entries now reserve child-list space before writes and scans are stable on files previously triggering crashes
• compile bundled DuckHTS extension sources with -Wpedantic during Unix and Windows package builds while leaving vendored htslib on its upstream warning flags
• fix the bundled non-Emscripten wasm_http_hfile.c translation unit so native package builds do not warn about an empty source file under pedantic C diagnostics
• harden Windows configure.win libcurl detection: the package now requires a successful curl_easy_init link using the detected pkg-config libcurl dependency closure before enabling htslib remote URL support, and otherwise disables libcurl/S3/GCS cleanly

Rduckhts 1.2.0-0.1.0 (2026-05-07)

• expose richer bundled GFF/GTF parsed attribute outputs through rduckhts_gff() / rduckhts_gtf() and multi-file wrappers: attributes_list = TRUE returns MAP(VARCHAR, VARCHAR[]) with grouped multi-values and GFF3 percent-decoding, while attributes_pairs = TRUE returns LIST<STRUCT(key VARCHAR, value VARCHAR, idx INTEGER)> for exact key/value/index records; attributes_map = TRUE remains the backward-compatible raw scalar map
• expose bundled read_gff(..., strict := true) through rduckhts_gff(strict = TRUE) and rduckhts_gff_multi(strict = TRUE), enabling GFF3 structural validation from R/DBI workflows, including wrong field counts and malformed attribute segments, while keeping the default GFF reader permissive for existing ingestion pipelines
• extend bundled rduckhts_score() / bcftools_score(...) so summary_path can be a character vector or callers can use summaries_list_file; multiple TSV/SSF summaries are scored in one genotype scan, log_path can write per-PRS matching/audit counts for loaded, matched, allele-mismatch, and duplicate markers, summaries_list_file directory scans are deterministic and ignore index sidecars, generated score/count column names are validated for uniqueness, and score accumulation now follows upstream bcftools +score float32 summation more closely
• collapse the generated package README function catalog behind a disclosure widget so package users can jump to quick-start and workflow examples more easily
• refresh the package README release docs: clarify the bundled htslib 1.23.1/system-requirements wording and redact transient temp-file paths in rendered example output so regenerated README diffs stay deterministic
• add bundled duckhts_cgranges_overlaps_list(...), a vectorized scalar overlap expander that returns LIST-of-STRUCT hit records so DBI queries can expand provider rows with UNNEST(...) without generated bulk-probe SQL; package tests cover one-row-per-hit expansion over regular tables and bundled BED data, and the existing duckhts_cgranges_overlaps_bulk(...) probe path now also handles DuckDB string vector lengths safely
• fix bundled duckhts_cgranges_from_query(...) ingestion of DuckDB string vectors by respecting string lengths instead of assuming NUL-terminated buffers; this fixes cgranges construction from providers such as read_bed(...) with longer chromosome names and adds package regression coverage
• add bundled vectorized scalar cgranges probe helpers duckhts_cgranges_has_overlap(...) and duckhts_cgranges_count_overlaps(...), enabling DBI queries to stream provider rows through an already-finalized session cgranges index for filtering/count annotations without the materializing overlaps_bulk query-string path; add package-level coverage for overlap, contain, and NULL probe semantics
• add bundled duckhts_cgranges_overlaps_bulk(...) for SQL-first bulk cgranges probing from R/DBI sessions: one table-function call now streams a query of probe intervals through a finalized cgranges index, supports mode = 'overlap'|'contain', accepts an optional query_row_id_col, and otherwise emits 1-based probe ordinals as query_row_id; add package-level regression coverage for the new bulk path
• document bundled duckhts_cgranges_* entry points in the generated function catalog and package README, add bundled DBI smoke coverage for the session-scoped cgranges registry API, and include a packaged overlap-conformance script reference for bedtk-style parity checks
• fix bundled rduckhts_fasta_nuc() / fasta_nuc(...) GC and AT percentages for intervals containing N: pct_gc and pct_at now use only informative A/C/G/T bases in the denominator, so ambiguous bases no longer depress reported bin/interval composition percentages; add bundled regression coverage
• add bundled C-built cgranges bulk-ingest support via duckhts_cgranges_from_query(...), which runs the source query on an extension-owned DuckDB connection and builds the cgranges index in C before publishing it to the session registry; duckhts_cgranges_from_table(...) remains deferred for now
• bundle htslib 1.23.1 in the package for the upstream CRAM decoder and GZI validation security fixes, including the wasm/browser-exposed parsing path shipped through Rduckhts
• add rduckhts_bam_bed_coverage(), bundling native duckhts_bam_bed_coverage(...) for samtools coverage-like regional summaries over BED targets with DuckHTS-specific pre/post-filter columns and read-mode strand-specific post summaries; bundled SQL/tinytest coverage now checks expected outputs on the packaged mixed BAM fixture, and fragment_mode / processing_threads are exposed but currently reserved for later phases
• reduce bundled rduckhts_bam_bed_coverage() / duckhts_bam_bed_coverage(...) peak memory by allocating and freeing per-region working depth buffers during scan processing instead of retaining them for the whole BED, tile large target intervals internally when computing covered-base breadth, keep the tiled implementation single-pass, align min_depth > 1 mean-depth behavior with samtools coverage, and expose decompression_threads so package callers can set htslib BAM/CRAM decode worker counts explicitly
• add rduckhts_samtools_idxstats(), bundling native duckhts_samtools_idxstats(...) for samtools idxstats-compatible BAM/CRAM/SAM summaries with indexed BAM fast-paths and scan fallback; package SQL/tinytest coverage now checks BAM fast-path output, CRAM fallback output, explicit index_path, and overwrite errors
• improve package-source hygiene for local development: ignore generated README.html, .Rcheck, staged duckhts_extension/htslib build outputs, wasm/webR harness byproducts, and stray root-level index files under r/Rduckhts/; add top-level make clean_local to purge the reproducible package-side artifacts
• add processing_threads parameter to rduckhts_mosdepth() and bundled duckhts_mosdepth(...) for parallel contig processing: workers claim contigs atomically and write output in header order; on the NA12878 WGS benchmark with 2 processing threads, fast mode is 1.38x faster, default mode 1.40x faster, and fragment mode 1.61x faster than mosdepth v0.3.13, all byte-identical; new default is processing_threads = 2
• change rduckhts_mosdepth() defaults to threads = 2 (decompression) and processing_threads = 2 (parallel contigs) for better out-of-the-box WGS performance
• ship htslib public headers and static library in the installed package under duckhts_extension/htslib/{include,lib}/; add inst/htslib_config.R (generated from htslib_config.R.in at configure time) providing htslib_cflags(), htslib_libs(), htslib_rpath(), and htslib_version() for downstream R packages that link against the bundled htslib
• fix configure.win to stage htslib headers into include/htslib/ alongside lib/, matching Unix configure
• change bundled bam_bin_counts(...) / rduckhts_bam_bin_counts() to return a dense fixed-bin layout across each selected contig span, including zero-count bins up to the contig end instead of only observed bins; this gives downstream CNV/sample serializers stable per-contig bin shapes, and the package docs/tests now describe and validate the dense contract
• add rduckhts_bam_bin_counts() and bundle native bam_bin_counts(...) fixed-width BAM/CRAM binning in the package. The new wrapper exposes mapq, require_flags, exclude_flags, and rmdup = "none"|"flag"|"streaming" duplicate handling, always returns per-bin forward/reverse totals, and can add per-bin GC/MAPQ summaries via stats = "gc", "mq", or "gc,mq"; bundled extdata now includes the tiny WisecondorX BAM/CRAM fixtures used by the new SQL/R tests, and the package README now includes a native bin-count example
• add rduckhts_mosdepth() examples to the package README, including windowed fragment coverage output and preview of the generated BED.gz regions file, and refresh the generated function-catalog text so the packaged mosdepth description matches the current v0.3.13 parity surface
• Expand rduckhts_mosdepth() and bundled duckhts_mosdepth(...) to cover the pinned local mosdepth 0.3.13 option surface for indexed BAM/CRAM input: fragment_mode = TRUE now matches upstream --fragment-mode full-fragment insert coverage for proper pairs, default mode is supported with CIGAR-aware coverage plus mate-overlap correction, read_groups = "..." filters RG tags, min_frag_len / max_frag_len filter absolute template length, and use_median = TRUE switches by = "<window|bed>" outputs from mean to median; add bundled SQL/R/conformance coverage for BAM and CRAM fast/fragment/default/median cases.
• Expand rduckhts_mosdepth() and bundled duckhts_mosdepth(...) fast-mode parity with quantize = "...", writing mosdepth-style .quantized.bed.gz + CSI output, and add bundled tests for quantized output plus explicit by = "<bed>" validation.
• Expand rduckhts_mosdepth() and bundled duckhts_mosdepth(...) fast-mode parity with thresholds = "..." for by = "<window|bed>", writing mosdepth-style .thresholds.bed.gz + CSI outputs; also align window/BED mean accumulation and window-region distribution bucketing with upstream mosdepth’s current implementation behavior, and add bundled SQL/R/native-conformance coverage for the new outputs.
• Bundle upstream mosdepth edge-case fixtures (big, empty-tids, overlapping-pairs, ovl, nanopore, and related BED files) in inst/extdata/ for stronger mosdepth parity testing, and record Brent Pedersen as the original mosdepth author in the package metadata/copyright bundle.
• Expand rduckhts_mosdepth() and bundled duckhts_mosdepth(...): the native mosdepth-compatible fast-mode rewrite now accepts indexed CRAM input via fasta = ... when required by htslib, and exposes precision_digits = 2 as an explicit wrapper argument instead of relying on the MOSDEPTH_PRECISION environment variable; add bundled BAM/CRAM tests plus explicit precision validation.
• Expand README.Rmd with runnable compression/indexing examples covering rduckhts_bgzip(), rduckhts_bgunzip(), rduckhts_bam_index(), rduckhts_bcf_index(), and rduckhts_tabix_index(), then regenerate the rendered package README outputs.
• Add decompression_threads to rduckhts_bam() and rduckhts_bam_multi(), matching the bundled read_bam(..., decompression_threads := 2) SQL parameter. The previous hardcoded htslib worker-thread count is now the documented default, and 0 disables per-file worker threads.
• Speed up bundled zero-column COUNT(*) queries across the HTS readers: read_bam(...), read_bcf(...), read_tabix(...), read_gff(...), read_gtf(...), and indexed read_bed(...) now use index metadata for full-file count-only scans when DuckDB projects no output columns; read_fasta(...) uses faidx sequence counts when an index is available and otherwise counts FASTA headers directly; read_fastq(...) continues to count raw FASTQ records directly when no projected columns are needed, while preserving paired/interleaved validation errors.
• Add multi-file reading wrappers: rduckhts_bam_multi, rduckhts_bcf_multi, rduckhts_fastq_multi, rduckhts_fasta_multi, rduckhts_bed_multi, rduckhts_tabix_multi, rduckhts_gff_multi, rduckhts_gtf_multi. Each follows the standard (con, table_name, files, ..., overwrite) convention, creates a DuckDB table with a filename column, and accepts an optional .params data.frame for per-file parameter overrides (e.g. per-sample regions or index paths). File expansion uses DuckDB’s glob() so S3 URLs work transparently.
• Add bundled hts_union_query(reader, pattern, params) SQL scalar macro for pure-SQL multi-file reading via SELECT * FROM query(hts_union_query('read_bam', '*.bam')).
• Clarify the package README’s browser/webR documentation: README.Rmd now covers the full Module.duckhtsWasmHttpConfig parameter set (headers, allowHosts, enforceHostAllowlist, withCredentials, allowInsecureAuth), explicitly notes that webR consumers can set that config from R via webr::eval_js() without editing the host page, and covers practical wasm/browser behaviors such as same-origin setup, CORS requirements, .csi to .tbi fallback, and non-fatal Range warnings under the local http.server harness.
• Use one extension-owned Emscripten compatibility header in the package wasm/webR build: configure now includes the shared header from src/include/ via the bootstrapped inst/duckhts_extension/include/wasm_socket_compat.h copy, keeping the bundled browser build aligned with the extension sources without changing native package builds.
• Make the bundled wasm extension self-contained with respect to htslib: the Emscripten/webR configure path now builds only libhts.a, links duckhts.duckdb_extension directly against that static archive, and no longer relies on runtime loading of bundled libhts.so* files in webR/browser environments.
• Add a browser-native wasm http / https backend in the bundled extension: src/wasm_http_hfile.c now registers a synchronous XHR-backed htslib scheme handler from the DuckDB extension entry point, so browser wasm builds can read same-origin and CORS-enabled remote HTS URLs without going through libcurl sockets.
• Keep wasm libcurl disabled in configure: r-wasm/webr ships /opt/webr/wasm/lib/libcurl.a and the emcc link test against it passes, but libcurl’s connect() calls from a SIDE_MODULE still trigger a webR Emscripten message-bus error (resolved is not a function) on first network use, so the package-owned XHR backend is the supported wasm HTTP path.
• Harden wasm browser HTTP range behavior in the bundled extension: wasm_http_hfile.c now caches object sizes from Content-Range/Content-Length, clamps range requests when size is known, short-circuits reads at/after EOF, and uses a GET Range: bytes=0-0 fallback for SEEK_END size discovery when HEAD metadata is unavailable; this avoids cross-origin 416 failures on .tbi index EOF probes (including GTEx tabix in webR/browser).
• Harden non-Range wasm/browser HTTP fallback in the bundled extension: when ranged reads receive 200 OK, wasm_http_hfile.c now caches the full object per open handle and serves later reads from that in-memory cache to avoid repeated full downloads, while still emitting one-time warnings when Range is ignored and when large fallback payloads (>=64 MiB) are used.
• Add optional wasm/browser request-header configuration in the bundled extension via Module.duckhtsWasmHttpConfig: supports custom headers (including bearer auth), host allowlisting, optional withCredentials, and a default HTTPS-only guard that blocks Authorization on non-HTTPS URLs unless allowInsecureAuth is explicitly enabled.
• Extend Module.duckhtsWasmHttpConfig with enforceHostAllowlist in the bundled wasm backend: when enabled, requests to hosts outside allowHosts are blocked instead of merely omitting configured headers.
• Fix the bundled wasm side-module final link during configure: preserve webR/Emscripten ${LDFLAGS} on the final duckhts.duckdb_extension link so the SIDE_MODULE settings reach the extension itself, and export duckhts_init_c_api explicitly for DuckDB’s loader. This fixes webR/browser rduckhts_load() failures where DuckDB could not find a usable init export in duckhts.duckdb_extension.
• Set the bundled extension metadata platform to linux_i686_musl for the Emscripten/webR path in configure, matching the platform value you are using for browser-side loading tests.
• Fix Wasm package builds under rwasm / r-universe: the package configure script now preserves injected NAME=VALUE cache overrides, forwards explicit --build / --host triplets into the vendored htslib ./configure, forwards webR’s Emscripten port flags for zlib/bzip2, seeds wasm-safe Autoconf cache results for zlib/bzip2/socket probes, injects a tiny Emscripten-only socket compatibility shim for recv/send/closesocket, and disables the optional htslib features that are not available in the stock webR/r-universe wasm toolchain (libcurl, S3, GCS, lzma, plugins); this fixes the original ac_cv_func_getrandom=no: command not found failure and the subsequent nested htslib cross-compile probe failures without changing native configure behavior.
• Fix bundled wasm extension artifacts: the package/browser wasm build now includes vendored htslib in the linked archive, avoiding unresolved symbols such as bcf_readrec at LOAD.

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.
• Fix bundled Windows builds under MinGW and Rtools: vendored htslib configuration now distinguishes windows_amd64_mingw from windows_amd64_rtools, keeping the smaller configure.win-style library set on MinGW while restoring the fuller static libcurl dependency closure needed on Rtools. CURL_STATICLIB remains on built objects rather than ./configure probes.
• Fix bundled Windows windows_amd64_rtools builds: the package build now pins CC/AR/RANLIB from R CMD config, avoiding mixed compiler/library selection when vendored htslib is configured, and keeps the MinGW static-libcurl configuration aligned with 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.

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