# 'DuckDB' High Throughput Sequencing File Formats Reader Extension

## Documentation for package ‘Rduckhts’ version 1.5.1-0.1.3

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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 | Build the duckhts DuckDB extension
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_bcftools_norm | Normalize Variant Alleles with bcftools-style Semantics
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_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_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_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_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_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 | DuckHTS SIMD backend diagnostics
rduckhts_simd_backend_available | DuckHTS SIMD backend diagnostics
rduckhts_simd_backend_compiled | DuckHTS SIMD backend diagnostics
rduckhts_simd_backend_cpu_supported | DuckHTS SIMD backend diagnostics
rduckhts_simd_info | DuckHTS SIMD backend diagnostics
rduckhts_simd_kernel_info | DuckHTS SIMD backend diagnostics
rduckhts_simd_requested_backend | DuckHTS SIMD backend diagnostics
rduckhts_simd_set_backend | DuckHTS SIMD backend diagnostics
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