Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API <https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.
| Version: | 2.0.0.0.1.9 |
| Depends: | R (≥ 4.4.0) |
| Imports: | DBI, duckdb (≥ 1.5.0), methods, utils |
| Suggests: | Rtinycc, tinytest |
| Published: | 2026-10-20 |
| DOI: | 10.32614/CRAN.package.Rduckhts |
| Author: | Sounkou Mahamane Toure [aut, cre], Ryan Ward [aut] (GenBank reader and FASTA converter), Nurture Bio [cph] (GenBank reader and FASTA converter), James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan, Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] (Htslib Authors), DuckHTS Contributors [cph] (DuckHTS DuckDB extension (MIT)), RBCFTools Authors [cph] (Copyright notice in bcf_reader.c), Genome Research Ltd [cph] (HTSlib, htscodecs and the bcftools filter engine (Petr Danecek)), Broad Institute [cph] (Portions of HTSlib), Massachusetts Institute of Technology [cph] (Portions of HTSlib), Medical Research Council [cph] (Portions of HTSlib CRAM code), Attractive Chaos [cph] (khash, kseq and related HTSlib and cgranges headers), Dana-Farber Cancer Institute [cph] (cgranges), Brent Pedersen [cph] (Original author of mosdepth and Somalier), Giulio Genovese [cph] (Author of BCFTools munge,score,liftover plugins), GENOMICS plc [cph] (VariantKey and RegionKey C API), Nicola Asuni [cph] (Author of the VariantKey and RegionKey C API), Devon Ryan [cph] (Author of libBigWig), Stichting DuckDB Foundation [cph] (DuckDB C extension API headers) |
| Maintainer: | Sounkou Mahamane Toure <sounkoutoure at gmail.com> |
| BugReports: | https://github.com/RGenomicsETL/duckhts/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Copyright: | See inst/COPYRIGHT |
| URL: | https://github.com/RGenomicsETL/duckhts, https://rgenomicsetl.r-universe.dev/Rduckhts |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make, cmake, zlib, libbz2, liblzma, libcurl, openssl (development headers) |
| Materials: | NEWS |
| CRAN checks: | Rduckhts results [issues need fixing before 2026-11-11] |
| Reference manual: | Rduckhts.html , Rduckhts.pdf |
| Package source: | Rduckhts_2.0.0.0.1.9.tar.gz |
| Windows binaries: | r-devel: Rduckhts_1.5.2-0.1.5.zip, r-release: Rduckhts_2.0.0.0.1.9.zip, r-oldrel: Rduckhts_2.0.0.0.1.9.zip |
| macOS binaries: | r-release (arm64): Rduckhts_2.0.0.0.1.9.tgz, r-oldrel (arm64): Rduckhts_2.0.0.0.1.9.tgz, r-release (x86_64): Rduckhts_2.0.0.0.1.9.tgz, r-oldrel (x86_64): Rduckhts_2.0.0.0.1.9.tgz |
| Old sources: | Rduckhts archive |
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