'DuckDB' High Throughput Sequencing File Formats Reader Extension

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) . VariantKey / RegionKey support follows Nicola Asuni (2018) .


Reference manual

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install.packages("Rduckhts")

2.0.2.0.1.1 by Sounkou Mahamane Toure, 5 days ago


https://github.com/RGenomicsETL/duckhts, https://rgenomicsetl.r-universe.dev/Rduckhts


Report a bug at https://github.com/RGenomicsETL/duckhts/issues


Browse source code at https://github.com/cran/Rduckhts


Authors: 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)


Documentation:   PDF Manual  


GPL (>= 2) license


Imports DBI, duckdb, methods, utils

Suggests Rtinycc, tinytest

System requirements: GNU make, cmake, zlib, libbz2, liblzma, libcurl, openssl (development headers)


See at CRAN