{ "_id": "6ae24d4b95ca2370cc8cca48", "Package": "Rduckhts", "Title": "'DuckDB' High Throughput Sequencing File Formats Reader\nExtension", "Version": "2.0.2.0.1.1", "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\",\nemail = \"sounkoutoure@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(given = \"Ryan\", family = \"Ward\",\nemail = \"ryan@nurture.bio\",\nrole = \"aut\", comment = \"GenBank reader and FASTA converter\"),\nperson(\"Nurture Bio\", role = \"cph\", comment = \"GenBank reader and FASTA converter\"),\nperson(given = \"James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan, Andrew Whitwham,Thomas Keane , Robert M Davies\", role = \"ctb\", comment = \"Htslib Authors\"),\nperson(\"DuckHTS Contributors\", role = \"cph\", comment = \"DuckHTS DuckDB extension (MIT)\"),\nperson(\"RBCFTools Authors\", role = \"cph\", comment = \"Copyright notice in bcf_reader.c\"),\nperson(\"Genome Research Ltd\", role = \"cph\", comment = \"HTSlib, htscodecs and the bcftools filter engine (Petr Danecek)\"),\nperson(\"Broad Institute\", role = \"cph\", comment = \"Portions of HTSlib\"),\nperson(\"Massachusetts Institute of Technology\", role = \"cph\", comment = \"Portions of HTSlib\"),\nperson(\"Medical Research Council\", role = \"cph\", comment = \"Portions of HTSlib CRAM code\"),\nperson(\"Attractive Chaos\", role = \"cph\", comment = \"khash, kseq and related HTSlib and cgranges headers\"),\nperson(\"Dana-Farber Cancer Institute\", role = \"cph\", comment = \"cgranges\"),\nperson(given = \"Brent\", family = \"Pedersen\", role = \"cph\", comment = \"Original author of mosdepth and Somalier\"),\nperson(given = \"Giulio\", family = \"Genovese\", email = \"giulio.genovese@gmail.com\", role = \"cph\", comment = \"Author of BCFTools munge,score,liftover plugins\"),\nperson(\"GENOMICS plc\", role = \"cph\", comment = \"VariantKey and RegionKey C API\"),\nperson(given = \"Nicola\", family = \"Asuni\", role = \"cph\", comment = \"Author of the VariantKey and RegionKey C API\"),\nperson(given = \"Devon\", family = \"Ryan\", role = \"cph\", comment = \"Author of libBigWig\"),\nperson(\"Stichting DuckDB Foundation\", role = \"cph\", comment = \"DuckDB C extension API headers\")\n)", "Description": "Bundles the 'duckhts' 'DuckDB' extension for reading High\nThroughput Sequencing file formats with 'DuckDB'. The 'DuckDB'\nC extension API \nand its 'htslib' dependency are compiled from vendored sources\nduring package installation. James K Bonfield and co-authors\n(2021) . VariantKey /\nRegionKey support follows Nicola Asuni (2018)\n.", "License": "GPL (>= 2)", "Copyright": "See inst/COPYRIGHT", "Encoding": "UTF-8", "SystemRequirements": "GNU make, cmake, zlib, libbz2, liblzma, libcurl,\nopenssl (development headers)", "NeedsCompilation": "yes", "URL": "https://github.com/RGenomicsETL/duckhts,\nhttps://rgenomicsetl.r-universe.dev/Rduckhts", "BugReports": "https://github.com/RGenomicsETL/duckhts/issues", "Config/roxygen2/version": "8.0.0", "Packaged": { "Date": "2026-10-28 19:19:24 UTC", "User": "root" }, "Author": "Sounkou Mahamane Toure [aut, cre], Ryan Ward [aut] (GenBank\nreader and FASTA converter), Nurture Bio [cph] (GenBank reader\nand FASTA converter), James K Bonfield, John Marshall,Petr\nDanecek ,Heng Li , Valeriu Ohan, Andrew Whitwham,Thomas Keane ,\nRobert M Davies [ctb] (Htslib Authors), DuckHTS Contributors\n[cph] (DuckHTS DuckDB extension (MIT)), RBCFTools Authors [cph]\n(Copyright notice in bcf_reader.c), Genome Research Ltd 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"rduckhts_bcftools_norm", "rduckhts_bed", "rduckhts_bed_multi", "rduckhts_bgunzip", "rduckhts_bgzip", "rduckhts_bigwig", "rduckhts_connect", "rduckhts_count_error_fit", "rduckhts_count_mixture_lowpass", "rduckhts_depth_bins", "rduckhts_depth_region_fraction", "rduckhts_depth_sex_fraction", "rduckhts_depth_state_segments", "rduckhts_depth_state_solutions", "rduckhts_detect_quality_encoding", "rduckhts_fasta", "rduckhts_fasta_index", "rduckhts_fasta_multi", "rduckhts_fasta_nuc", "rduckhts_fastq", "rduckhts_fastq_multi", "rduckhts_functions", "rduckhts_genbank", "rduckhts_genbank_to_fasta", "rduckhts_geno", "rduckhts_geno_sites", "rduckhts_gff", "rduckhts_gff_convert_parquet", "rduckhts_gff_multi", "rduckhts_gtf", "rduckhts_gtf_multi", "rduckhts_hts_header", "rduckhts_hts_index", "rduckhts_hts_index_raw", "rduckhts_hts_index_spans", "rduckhts_htslib_config", "rduckhts_htslib_info", "rduckhts_htslib_version", "rduckhts_install_macros", "rduckhts_liftover", "rduckhts_load", "rduckhts_mosdepth", "rduckhts_munge", "rduckhts_pileup", "rduckhts_roh", "rduckhts_roh_counts", "rduckhts_samtools_idxstats", "rduckhts_score", "rduckhts_simd_backend", "rduckhts_simd_backend_available", "rduckhts_simd_backend_compiled", "rduckhts_simd_backend_cpu_supported", "rduckhts_simd_info", "rduckhts_simd_kernel_info", "rduckhts_simd_requested_backend", "rduckhts_simd_set_backend", "rduckhts_somalier_bam_counts", "rduckhts_somalier_charr", "rduckhts_somalier_find_sites", "rduckhts_somalier_import_sites", "rduckhts_somalier_matched_contamination", "rduckhts_somalier_relatedness", "rduckhts_somalier_sex", "rduckhts_somalier_sketches", "rduckhts_somalier_vcf_counts", "rduckhts_tabix", "rduckhts_tabix_convert_parquet", "rduckhts_tabix_index", "rduckhts_tabix_multi", "setup_hts_env" ], "_help": [ { "page": "detect_complex_types", "title": "Detect Complex Types in DuckDB Table", "topics": [ "detect_complex_types" ] }, { "page": "duckdb_type_mappings", "title": "DuckDB to R Type Mappings", "topics": [ "duckdb_type_mappings" ] }, { "page": "duckhts_bootstrap", "title": "Bootstrap the duckhts extension sources into the R package", "topics": [ "duckhts_bootstrap" ] }, { "page": "duckhts_build", "title": "Retired manual DuckHTS extension builder", "topics": [ "duckhts_build" ] }, { "page": "duckhts_load", "title": "Load the duckhts extension into a DuckDB connection", "topics": [ "duckhts_load" ] }, { "page": "extract_array_element", "title": "Extract Array Elements Safely", "topics": [ "extract_array_element" ] }, { "page": "extract_map_data", "title": "Extract MAP Keys and Values", "topics": [ "extract_map_data" ] }, { "page": "normalize_tabix_types", "title": "Normalize R Data Types to DuckDB Types for Tabix", "topics": [ "normalize_tabix_types" ] }, { "page": "rduckhts_ancestry_bam", "title": "Project ancestry directly from an indexed BAM or CRAM", "topics": [ "rduckhts_ancestry_bam" ] }, { "page": "rduckhts_ancestry_geno", "title": "Estimate ancestry from a materialized `read_geno` relation", "topics": [ "rduckhts_ancestry_geno" ] }, { "page": "rduckhts_ancestry_panel", "title": "Create a deterministic ancestry site panel for BAM/CRAM counts", "topics": [ "rduckhts_ancestry_panel" ] }, { "page": "rduckhts_ancestry_proportions", "title": "Estimate projected ancestry proportions from frequency or dosage relations", "topics": [ "rduckhts_ancestry_proportions" ] }, { "page": "rduckhts_bam", "title": "Create SAM/BAM/CRAM Table", "topics": [ "rduckhts_bam" ] }, { "page": "rduckhts_bam_bed_coverage", "title": "Native BAM/CRAM BED Regional Coverage Summary", "topics": [ "rduckhts_bam_bed_coverage" ] }, { "page": "rduckhts_bam_bin_counts", "title": "Native Fixed-Width BAM/CRAM Bin Counts", "topics": [ "rduckhts_bam_bin_counts" ] }, { "page": "rduckhts_bam_convert_parquet", "title": "Convert SAM/BAM/CRAM reader output to Parquet with DuckHTS metadata", "topics": [ "rduckhts_bam_convert_parquet" ] }, { "page": "rduckhts_bam_index", "title": "Build BAM or CRAM Index", "topics": [ "rduckhts_bam_index" ] }, { "page": "rduckhts_bam_insert_size_counts", "title": "BAM/CRAM Insert-Size Counts", "topics": [ "rduckhts_bam_insert_size_counts", "rduckhts_bam_insert_size_counts_sql" ] }, { "page": "rduckhts_bam_mate_overlap_counts", "title": "Count Agreement Between Overlapping Mates", "topics": [ "rduckhts_bam_mate_overlap_counts" ] }, { "page": "rduckhts_bam_mismatch_counts", "title": "Count Aligned Bases Against the Reference", "topics": [ "rduckhts_bam_mismatch_counts" ] }, { "page": "rduckhts_bam_multi", "title": "Read multiple BAM/SAM files into a DuckDB table", "topics": [ "rduckhts_bam_multi" ] }, { "page": "rduckhts_bcf", "title": "Create VCF/BCF Table", "topics": [ "rduckhts_bcf" ] }, { "page": "rduckhts_bcf_convert_parquet", "title": "Convert VCF/BCF reader output to Parquet with DuckHTS metadata", "topics": [ "rduckhts_bcf_convert_parquet" ] }, { "page": "rduckhts_bcf_index", "title": "Build VCF or BCF Index", "topics": [ "rduckhts_bcf_index" ] }, { "page": "rduckhts_bcf_multi", "title": "Read multiple VCF/BCF files into a DuckDB table", "topics": [ "rduckhts_bcf_multi" ] }, { "page": "rduckhts_bcf_samples", "title": "Read the VCF/BCF Sample Catalog", "topics": [ "rduckhts_bcf_samples" ] }, { "page": "rduckhts_bcftools_norm", "title": "Normalize Variant Alleles with bcftools-style Semantics", "topics": [ "rduckhts_bcftools_norm" ] }, { "page": "rduckhts_bed", "title": "Create BED Table", "topics": [ "rduckhts_bed" ] }, { "page": "rduckhts_bed_multi", "title": "Read multiple BED files into a DuckDB table", "topics": [ "rduckhts_bed_multi" ] }, { "page": "rduckhts_bgunzip", "title": "BGZF Decompress a File", "topics": [ "rduckhts_bgunzip" ] }, { "page": "rduckhts_bgzip", "title": "BGZF Compress a File", "topics": [ "rduckhts_bgzip" ] }, { "page": "rduckhts_bigwig", "title": "Create a BigWig Signal Table", "topics": [ "rduckhts_bigwig" ] }, { "page": "rduckhts_connect", "title": "Create a DuckDB connection with bundled DuckHTS loaded", "topics": [ "rduckhts_connect" ] }, { "page": "rduckhts_count_error_fit", "title": "Fit Read Error and Contamination from Allele Read Counts", "topics": [ "rduckhts_count_error_fit" ] }, { "page": "rduckhts_count_mixture_lowpass", "title": "Estimate a Conditional Second-Genome Share from Low-Pass Counts", "topics": [ "rduckhts_count_mixture_lowpass" ] }, { "page": "rduckhts_depth_bins", "title": "Correct Bin Read Counts for GC Content", "topics": [ "rduckhts_depth_bins" ] }, { "page": "rduckhts_depth_region_fraction", "title": "Estimate the Share of Cells with a One-Copy Change of a Region", "topics": [ "rduckhts_depth_region_fraction" ] }, { "page": "rduckhts_depth_sex_fraction", "title": "Estimate the Share of a Second Genome of the Other Sex from X and Y Depth", "topics": [ "rduckhts_depth_sex_fraction" ] }, { "page": "rduckhts_depth_state_solutions", "title": "Decode Tumour Fraction, Ploidy and Copy-Number Segments from Corrected Bins", "topics": [ "rduckhts_depth_state_segments", "rduckhts_depth_state_solutions" ] }, { "page": "rduckhts_detect_quality_encoding", "title": "Detect FASTQ Quality Encoding", "topics": [ "rduckhts_detect_quality_encoding" ] }, { "page": "rduckhts_fasta", "title": "Create FASTA Table", "topics": [ "rduckhts_fasta" ] }, { "page": "rduckhts_fasta_index", "title": "Build FASTA Index", "topics": [ "rduckhts_fasta_index" ] }, { "page": "rduckhts_fasta_multi", "title": "Read multiple FASTA files into a DuckDB table", "topics": [ "rduckhts_fasta_multi" ] }, { "page": "rduckhts_fasta_nuc", "title": "Compute FASTA Interval Nucleotide Composition", "topics": [ "rduckhts_fasta_nuc" ] }, { "page": "rduckhts_fastq", "title": "Create FASTQ Table", "topics": [ "rduckhts_fastq" ] }, { "page": "rduckhts_fastq_multi", "title": "Read multiple FASTQ files into a DuckDB table", "topics": [ "rduckhts_fastq_multi" ] }, { "page": "rduckhts_functions", "title": "List DuckHTS Extension Functions", "topics": [ "rduckhts_functions" ] }, { "page": "rduckhts_genbank", "title": "Create GenBank Feature Table", "topics": [ "rduckhts_genbank" ] }, { "page": "rduckhts_genbank_to_fasta", "title": "Write GenBank Sequence as FASTA", "topics": [ "rduckhts_genbank_to_fasta" ] }, { "page": "rduckhts_geno", "title": "Read Record-Major Genotypes", "topics": [ "rduckhts_geno" ] }, { "page": "rduckhts_geno_sites", "title": "Fetch Exact Alleles at Requested Sites", "topics": [ "rduckhts_geno_sites" ] }, { "page": "rduckhts_gff", "title": "Create GFF3 Table", "topics": [ "rduckhts_gff" ] }, { "page": "rduckhts_gff_convert_parquet", "title": "Convert GFF3 reader output to Parquet with DuckHTS metadata", "topics": [ "rduckhts_gff_convert_parquet" ] }, { "page": "rduckhts_gff_multi", "title": "Read multiple GFF files into a DuckDB table", "topics": [ "rduckhts_gff_multi" ] }, { "page": "rduckhts_gtf", "title": "Create GTF Table", "topics": [ "rduckhts_gtf" ] }, { "page": "rduckhts_gtf_multi", "title": "Read multiple GTF files into a DuckDB table", "topics": [ "rduckhts_gtf_multi" ] }, { "page": "rduckhts_hts_header", "title": "Read HTS Header Metadata", "topics": [ "rduckhts_hts_header" ] }, { "page": "rduckhts_hts_index", "title": "Read HTS Index Metadata", "topics": [ "rduckhts_hts_index" ] }, { "page": "rduckhts_hts_index_raw", "title": "Read Raw HTS Index Blob", "topics": [ "rduckhts_hts_index_raw" ] }, { "page": "rduckhts_hts_index_spans", "title": "Read HTS Index Spans", "topics": [ "rduckhts_hts_index_spans" ] }, { "page": "rduckhts_htslib_config", "title": "Get the Installed htslib Linking Contract", "topics": [ "rduckhts_htslib_config" ] }, { "page": "rduckhts_htslib_info", "title": "Inspect the Loaded htslib Build", "topics": [ "rduckhts_htslib_info" ] }, { "page": "rduckhts_htslib_version", "title": "Return the Loaded htslib Version", "topics": [ "rduckhts_htslib_version" ] }, { "page": "rduckhts_install_macros", "title": "Install DuckHTS macros on a connection", "topics": [ "rduckhts_install_macros" ] }, { "page": "rduckhts_liftover", "title": "Lift Over Variant Coordinates Against a Query", "topics": [ "rduckhts_liftover" ] }, { "page": "rduckhts_load", "title": "Load DuckHTS Extension", "topics": [ "rduckhts_load" ] }, { "page": "rduckhts_mosdepth", "title": "Native mosdepth-Compatible Coverage Outputs", "topics": [ "rduckhts_mosdepth" ] }, { "page": "rduckhts_munge", "title": "Munge Summary Statistics Rows", "topics": [ "rduckhts_munge" ] }, { "page": "rduckhts_pileup", "title": "Create BAM Pileup Table", "topics": [ "rduckhts_pileup" ] }, { "page": "rduckhts_roh", "title": "Find Runs of Homozygosity", "topics": [ "rduckhts_roh" ] }, { "page": "rduckhts_roh_counts", "title": "Find Runs of Homozygosity from Read Counts", "topics": [ "rduckhts_roh_counts" ] }, { "page": "rduckhts_samtools_idxstats", "title": "samtools idxstats-Compatible Alignment Summary", "topics": [ "rduckhts_samtools_idxstats" ] }, { "page": "rduckhts_score", "title": "Compute 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