Package index • Rduckhts

All functions

detect_complex_types(): Detect Complex Types in DuckDB Table
duckdb_type_mappings(): DuckDB to R Type Mappings
duckhts_bootstrap(): Bootstrap the duckhts extension sources into the R package
duckhts_build(): Retired manual DuckHTS extension builder
duckhts_load(): Load the duckhts extension into a DuckDB connection
extract_array_element(): Extract Array Elements Safely
extract_map_data(): Extract MAP Keys and Values
normalize_tabix_types(): Normalize R Data Types to DuckDB Types for Tabix
rduckhts_bam(): Create SAM/BAM/CRAM Table
rduckhts_bam_bed_coverage(): Native BAM/CRAM BED Regional Coverage Summary
rduckhts_bam_bin_counts(): Native Fixed-Width BAM/CRAM Bin Counts
rduckhts_bam_convert_parquet(): Convert SAM/BAM/CRAM reader output to Parquet with DuckHTS metadata
rduckhts_bam_index(): Build BAM or CRAM Index
rduckhts_bam_multi(): Read multiple BAM/SAM files into a DuckDB table
rduckhts_bcf(): Create VCF/BCF Table
rduckhts_bcf_convert_parquet(): Convert VCF/BCF reader output to Parquet with DuckHTS metadata
rduckhts_bcf_index(): Build VCF or BCF Index
rduckhts_bcf_multi(): Read multiple VCF/BCF files into a DuckDB table
rduckhts_bcf_samples(): Read the VCF/BCF Sample Catalog
rduckhts_bcftools_norm(): Normalize Variant Alleles with bcftools-style Semantics
rduckhts_bed(): Create BED Table
rduckhts_bed_multi(): Read multiple BED files into a DuckDB table
rduckhts_bgunzip(): BGZF Decompress a File
rduckhts_bgzip(): BGZF Compress a File
rduckhts_bigwig(): Create a BigWig Signal Table
rduckhts_connect(): Create a DuckDB connection with bundled DuckHTS loaded
rduckhts_detect_quality_encoding(): Detect FASTQ Quality Encoding
rduckhts_fasta(): Create FASTA Table
rduckhts_fasta_index(): Build FASTA Index
rduckhts_fasta_multi(): Read multiple FASTA files into a DuckDB table
rduckhts_fasta_nuc(): Compute FASTA Interval Nucleotide Composition
rduckhts_fastq(): Create FASTQ Table
rduckhts_fastq_multi(): Read multiple FASTQ files into a DuckDB table
rduckhts_functions(): List DuckHTS Extension Functions
rduckhts_genbank(): Create GenBank Feature Table
rduckhts_genbank_to_fasta(): Write GenBank Sequence as FASTA
rduckhts_geno(): Read Record-Major Genotypes
rduckhts_gff(): Create GFF3 Table
rduckhts_gff_convert_parquet(): Convert GFF3 reader output to Parquet with DuckHTS metadata
rduckhts_gff_multi(): Read multiple GFF files into a DuckDB table
rduckhts_gtf(): Create GTF Table
rduckhts_gtf_multi(): Read multiple GTF files into a DuckDB table
rduckhts_haplotypes(): Replay Phased Transcript Haplotypes
rduckhts_hts_header(): Read HTS Header Metadata
rduckhts_hts_index(): Read HTS Index Metadata
rduckhts_hts_index_raw(): Read Raw HTS Index Blob
rduckhts_hts_index_spans(): Read HTS Index Spans
rduckhts_htslib_config(): Get the Installed htslib Linking Contract
rduckhts_htslib_info(): Inspect the Loaded htslib Build
rduckhts_htslib_version(): Return the Loaded htslib Version
rduckhts_liftover(): Lift Over Variant Coordinates Against a Query
rduckhts_load(): Load DuckHTS Extension
rduckhts_mosdepth(): Native mosdepth-Compatible Coverage Outputs
rduckhts_munge(): Munge Summary Statistics Rows
rduckhts_pileup(): Create BAM Pileup Table
rduckhts_samtools_idxstats(): samtools idxstats-Compatible Alignment Summary
rduckhts_score(): Compute Polygenic Scores
rduckhts_simd_backend() rduckhts_simd_requested_backend() rduckhts_simd_backend_compiled() rduckhts_simd_backend_cpu_supported() rduckhts_simd_backend_available() rduckhts_simd_info() rduckhts_simd_kernel_info() rduckhts_simd_set_backend(): DuckHTS SIMD backend diagnostics
rduckhts_somalier_bam_counts(): Extract Panel-Aligned Counts from BAM or CRAM
rduckhts_somalier_charr(): Estimate Per-Sample Contamination with CHARR
rduckhts_somalier_import_sites(): Import an Already Selected Somalier Sites VCF or BCF
rduckhts_somalier_matched_contamination(): Estimate Directional Contamination Against Matched Anchors
rduckhts_somalier_relatedness(): Compare Somalier-Derived Sample Sketches
rduckhts_somalier_sketches(): Prepare Somalier-Derived Sample Sketches
rduckhts_somalier_vcf_counts(): Extract Panel-Aligned Counts from VCF or BCF
rduckhts_tabix(): Create Tabix-Indexed File Table
rduckhts_tabix_convert_parquet(): Convert generic tabix reader output to Parquet with DuckHTS metadata
rduckhts_tabix_index(): Build Tabix Index
rduckhts_tabix_multi(): Read multiple tabix-indexed files into a DuckDB table
setup_hts_env(): Setup HTSlib Environment