Returns the package-bundled function catalog generated from the top-level
functions.yaml manifest in the duckhts repository.
Value
A data frame describing the extension functions, including the DuckDB function name, kind, category, signature, return type, optional R helper wrapper, short description, and example SQL.
Examples
catalog <- rduckhts_functions()
subset(catalog, category == "Sequence UDFs", select = c("name", "description"))
#> name
#> 122 seq_revcomp
#> 123 seq_canonical
#> 124 seq_hash_2bit
#> 125 seq_encode_4bit
#> 126 seq_decode_4bit
#> 127 seq_gc_content
#> 128 seq_kmers
#> description
#> 122 Compute the reverse complement of a DNA sequence using A, C, G, T, and N bases. Overloaded: accepts either a VARCHAR text sequence (returns VARCHAR) or a UTINYINT[] of htslib nt16 codes as produced by read_bam(sequence_encoding := 'nt16') (returns UTINYINT[]); the nt16 overload is bit-identical to the text path after decoding, so BAM pipelines can reverse-complement without leaving the nt16 encoding.
#> 123 Return the lexicographically smaller of a sequence and its reverse complement. Overloaded: accepts either a VARCHAR text sequence (returns VARCHAR) or a UTINYINT[] of htslib nt16 codes as produced by read_bam(sequence_encoding := 'nt16') (returns UTINYINT[]); the nt16 overload compares by decoded base order and is bit-identical to the text path after decoding.
#> 124 Encode a short DNA sequence as a 2-bit unsigned integer hash. Overloaded to also accept a UTINYINT[] of htslib nt16 codes (from read_bam(sequence_encoding := 'nt16')); non-ACGT codes yield NULL, bit-identical to the text path.
#> 125 Encode an IUPAC DNA sequence as a list of 4-bit base codes, preserving ambiguity symbols including N.
#> 126 Decode a list of 4-bit IUPAC DNA base codes back into a sequence string.
#> 127 Compute GC fraction for a DNA sequence as a value between 0 and 1. Overloaded: accepts either a VARCHAR text sequence or a UTINYINT[] of htslib nt16 codes as produced by read_bam(sequence_encoding := 'nt16'); the nt16 overload classifies codes directly and is bit-identical to the text path, so BAM pipelines can compute GC without decoding sequences back to text.
#> 128 Expand a sequence into positional k-mers with optional canonicalization.
subset(rduckhts_functions(kind = "table"), select = c("name", "r_wrapper"))
#> name r_wrapper
#> 1 duckhts_simd_info rduckhts_simd_info
#> 2 duckhts_simd_kernel_info rduckhts_simd_kernel_info
#> 3 duckhts_simd_set_backend rduckhts_simd_set_backend
#> 4 duckvep_model_load
#> 5 duckvep_haplotypes rduckhts_haplotypes
#> 6 duckvep_annotate
#> 7 duckvep_so_terms
#> 8 read_bcf rduckhts_bcf
#> 9 read_geno rduckhts_geno
#> 10 read_bcf_samples rduckhts_bcf_samples
#> 11 read_bam rduckhts_bam
#> 12 read_pileup rduckhts_pileup
#> 13 read_fasta rduckhts_fasta
#> 14 read_bed rduckhts_bed
#> 15 fasta_nuc rduckhts_fasta_nuc
#> 16 duckhts_cgranges_overlaps
#> 17 duckhts_cgranges_overlaps_bulk
#> 18 read_fastq rduckhts_fastq
#> 19 read_bigwig rduckhts_bigwig
#> 20 duckhts_somalier_bam_counts rduckhts_somalier_bam_counts
#> 21 detect_quality_encoding rduckhts_detect_quality_encoding
#> 22 read_gff rduckhts_gff
#> 23 read_gtf rduckhts_gtf
#> 24 read_genbank rduckhts_genbank
#> 25 genbank_to_fasta rduckhts_genbank_to_fasta
#> 26 read_tabix rduckhts_tabix
#> 27 fasta_index rduckhts_fasta_index
#> 28 bgzip rduckhts_bgzip
#> 29 bgunzip rduckhts_bgunzip
#> 30 bam_index rduckhts_bam_index
#> 31 bcf_index rduckhts_bcf_index
#> 32 tabix_index rduckhts_tabix_index
#> 33 bam_bin_counts rduckhts_bam_bin_counts
#> 34 duckhts_bam_bed_coverage rduckhts_bam_bed_coverage
#> 35 duckhts_mosdepth rduckhts_mosdepth
#> 36 duckhts_samtools_idxstats rduckhts_samtools_idxstats
#> 37 read_hts_header rduckhts_hts_header
#> 38 read_hts_index rduckhts_hts_index
#> 39 read_hts_index_spans rduckhts_hts_index_spans
#> 40 bcftools_score rduckhts_score
#> 41 seq_kmers