{ "_id": "6a2759cd24555f66ed5313ea", "Package": "Rduckhts", "Title": "'DuckDB' High Throughput Sequencing File Formats Reader\nExtension", "Version": "1.3.0.9000-0.1.0", "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\",\nemail = \"sounkoutoure@gmail.com\",\nrole = c(\"aut\", \"cre\")),\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(given = \"Brent\", family = \"Pedersen\", role = \"cph\", comment = \"Mosdepth Original Author\"),\nperson(given = \"Giulio\", family = \"Genovese\", email = \"giulio.genovese@gmail.com\", role = \"cph\", comment = \"Author of BCFTools munge,score,liftover plugins\"),\nperson(given = \"Nicola\", family = \"Asuni\", role = \"cph\", comment = \"Author of the VariantKey and RegionKey C API\"),\nperson(given = \"DuckDB C Extension API Authors\", role = \"ctb\")\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-3", "Copyright": "See inst/COPYRIGHT", "Encoding": "UTF-8", "SystemRequirements": "GNU make, cmake, zlib, libbz2, liblzma, libcurl,\nopenssl (development headers)", "RoxygenNote": "7.3.3", "URL": "https://github.com/RGenomicsETL/duckhts,\nhttps://rgenomicsetl.r-universe.dev/Rduckhts", "BugReports": "https://github.com/RGenomicsETL/duckhts/issues", "Config/pak/sysreqs": "cmake make libbz2-dev liblzma-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://rgenomicsetl.r-universe.dev", "Date/Publication": "2026-06-08 22:47:01 UTC", "RemoteUrl": "https://github.com/RGenomicsETL/duckhts", "RemoteRef": "HEAD", "RemoteSha": "734bf52d935074e2729fd9616845b00e84d7e8be", "RemoteSubdir": "r/Rduckhts", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-09 00:03:48 UTC", "User": "root" }, "Author": "Sounkou Mahamane Toure [aut, cre],\nJames K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu 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"topics": [ "normalize_tabix_types" ] }, { "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_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_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_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_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_liftover", "title": "Lift Over Variant Coordinates Against a Query", "topics": [ "rduckhts_liftover" ] }, { "page": "rduckhts_load", 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