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_ancestry_bam   Project ancestry directly from an indexed BAM
                        or CRAM
rduckhts_ancestry_geno
                        Estimate ancestry from a materialized
                        'read_geno' relation
rduckhts_ancestry_panel
                        Create a deterministic ancestry site panel for
                        BAM/CRAM counts
rduckhts_ancestry_proportions
                        Estimate projected ancestry proportions from
                        frequency or dosage relations
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_insert_size_counts
                        BAM/CRAM Insert-Size Counts
rduckhts_bam_mate_overlap_counts
                        Count Agreement Between Overlapping Mates
rduckhts_bam_mismatch_counts
                        Count Aligned Bases Against the Reference
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_count_error_fit
                        Fit Read Error and Contamination from Allele
                        Read Counts
rduckhts_count_mixture_lowpass
                        Estimate a Conditional Second-Genome Share from
                        Low-Pass Counts
rduckhts_depth_bins     Correct Bin Read Counts for GC Content
rduckhts_depth_region_fraction
                        Estimate the Share of Cells with a One-Copy
                        Change of a Region
rduckhts_depth_sex_fraction
                        Estimate the Share of a Second Genome of the
                        Other Sex from X and Y Depth
rduckhts_depth_state_solutions
                        Decode Tumour Fraction, Ploidy and Copy-Number
                        Segments from Corrected Bins
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_geno_sites     Fetch Exact Alleles at Requested Sites
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_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_install_macros
                        Install DuckHTS macros on a connection
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_roh            Find Runs of Homozygosity
rduckhts_roh_counts     Find Runs of Homozygosity from Read Counts
rduckhts_samtools_idxstats
                        samtools idxstats-Compatible Alignment Summary
rduckhts_score          Compute Polygenic Scores
rduckhts_simd_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_find_sites
                        Select a Somalier Panel from Population
                        Variants
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_sex   Infer X/Y Dosage Sex Evidence
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
