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.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.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.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.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.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.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.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.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.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.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.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.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.rduckhts_liftover(): variant coordinate liftover
backed by bcftools +liftover using UCSC chain files, with
full indel normalization, INFO/END lifting, and MT passthrough.rduckhts_bed() for BED3–BED12 interval files and
rduckhts_fasta_nuc() for nucleotide composition over BED
intervals or fixed-width bins.rduckhts_bgzip(),
rduckhts_bgunzip(), rduckhts_bam_index(),
rduckhts_bcf_index(), and
rduckhts_tabix_index().rduckhts_hts_header(),
rduckhts_hts_index(),
rduckhts_hts_index_spans(), and
rduckhts_hts_index_raw().rduckhts_bam() and
rduckhts_fastq() (quality_representation,
input_quality_encoding) and
rduckhts_detect_quality_encoding() for heuristic FASTQ
encoding detection.sequence_encoding := 'nt16' parameter to
rduckhts_bam(), rduckhts_fasta(), and
rduckhts_fastq() for raw htslib nt16 sequence output as
UTINYINT[].sam_flag_bits() and
sam_flag_has(), CIGAR utility functions, and
is_forward_aligned().Conditionaly enable plugins in windows
Updates the configure script to avoid check faillure on CRAN MacOS
Update the extension version to 0.1.3
duckhts
0.1.2.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.