Man pages for Rduckhts
'DuckDB' High Throughput Sequencing File Formats Reader Extension
| 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 | DuckDB HTS File Reader Extension for R |
| 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... |
| rduckhts_ancestry_proportions | Estimate projected ancestry proportions from frequency or... |
| 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... |
| 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... |
| 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... |
| 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... |
| rduckhts_depth_sex_fraction | Estimate the Share of a Second Genome of the Other Sex from X... |
| rduckhts_depth_state_solutions | Decode Tumour Fraction, Ploidy and Copy-Number Segments from... |
| 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... |
| rduckhts_tabix_index | Build Tabix Index |
| rduckhts_tabix_multi | Read multiple tabix-indexed files into a DuckDB table |
| setup_hts_env | Setup HTSlib Environment |
