'DuckDB' High Throughput Sequencing File Formats Reader Extension

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Documentation for package ‘Rduckhts’ version 1.2.1-0.1.0

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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_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_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_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_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_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_samtools_idxstats samtools idxstats-Compatible Alignment Summary
rduckhts_score Compute Polygenic Scores
rduckhts_tabix Create Tabix-Indexed File Table
rduckhts_tabix_index Build Tabix Index
rduckhts_tabix_multi Read multiple tabix-indexed files into a DuckDB table
setup_hts_env Setup HTSlib Environment