Package: Rduckhts 1.3.0.9000-0.1.0

Sounkou Mahamane Toure

Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API <https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.

Authors:Sounkou Mahamane Toure [aut, cre], James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan, Andrew Whitwham,Thomas Keane , Robert M Davies [ctb], Brent Pedersen [cph], Giulio Genovese [cph], Nicola Asuni [cph], DuckDB C Extension API Authors [ctb]

Rduckhts_1.3.0.9000-0.1.0.tar.gz
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Rduckhts_1.3.0.9000-0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rduckhts/json (API)

# Install 'Rduckhts' in R:
install.packages('Rduckhts', repos = c('https://rgenomicsetl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rgenomicsetl/duckhts/issues

On CRAN:

Conda:

bamduckdb-extensionfastqhtslibvcf

5.37 score 15 stars 13 scripts 377 downloads 60 exports 2 dependencies

Last updated from:122306d870. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK202
source / vignettesOK240
linux-release-x86_64OK205
macos-release-arm64OK129
macos-oldrel-arm64OK130
windows-develOK2465
windows-releaseOK251
windows-oldrelOK2978
wasm-releaseOK134

Exports:detect_complex_typesduckdb_type_mappingsduckhts_bootstrapduckhts_buildduckhts_loadextract_array_elementextract_map_datanormalize_tabix_typesrduckhts_bamrduckhts_bam_bed_coveragerduckhts_bam_bin_countsrduckhts_bam_convert_parquetrduckhts_bam_indexrduckhts_bam_multirduckhts_bcfrduckhts_bcf_convert_parquetrduckhts_bcf_indexrduckhts_bcf_multirduckhts_bcftools_normrduckhts_bedrduckhts_bed_multirduckhts_bgunziprduckhts_bgziprduckhts_detect_quality_encodingrduckhts_fastarduckhts_fasta_indexrduckhts_fasta_multirduckhts_fasta_nucrduckhts_fastqrduckhts_fastq_multirduckhts_functionsrduckhts_gffrduckhts_gff_convert_parquetrduckhts_gff_multirduckhts_gtfrduckhts_gtf_multirduckhts_hts_headerrduckhts_hts_indexrduckhts_hts_index_rawrduckhts_hts_index_spansrduckhts_liftoverrduckhts_loadrduckhts_mosdepthrduckhts_mungerduckhts_pileuprduckhts_samtools_idxstatsrduckhts_scorerduckhts_simd_backendrduckhts_simd_backend_availablerduckhts_simd_backend_compiledrduckhts_simd_backend_cpu_supportedrduckhts_simd_inforduckhts_simd_kernel_inforduckhts_simd_requested_backendrduckhts_simd_set_backendrduckhts_tabixrduckhts_tabix_convert_parquetrduckhts_tabix_indexrduckhts_tabix_multisetup_hts_env

Dependencies:DBIduckdb

Readme and manuals

Help Manual

Help pageTopics
Detect Complex Types in DuckDB Tabledetect_complex_types
DuckDB to R Type Mappingsduckdb_type_mappings
Bootstrap the duckhts extension sources into the R packageduckhts_bootstrap
Build the duckhts DuckDB extensionduckhts_build
Load the duckhts extension into a DuckDB connectionduckhts_load
Extract Array Elements Safelyextract_array_element
Extract MAP Keys and Valuesextract_map_data
Normalize R Data Types to DuckDB Types for Tabixnormalize_tabix_types
Create SAM/BAM/CRAM Tablerduckhts_bam
Native BAM/CRAM BED Regional Coverage Summaryrduckhts_bam_bed_coverage
Native Fixed-Width BAM/CRAM Bin Countsrduckhts_bam_bin_counts
Convert SAM/BAM/CRAM reader output to Parquet with DuckHTS metadatarduckhts_bam_convert_parquet
Build BAM or CRAM Indexrduckhts_bam_index
Read multiple BAM/SAM files into a DuckDB tablerduckhts_bam_multi
Create VCF/BCF Tablerduckhts_bcf
Convert VCF/BCF reader output to Parquet with DuckHTS metadatarduckhts_bcf_convert_parquet
Build VCF or BCF Indexrduckhts_bcf_index
Read multiple VCF/BCF files into a DuckDB tablerduckhts_bcf_multi
Normalize Variant Alleles with bcftools-style Semanticsrduckhts_bcftools_norm
Create BED Tablerduckhts_bed
Read multiple BED files into a DuckDB tablerduckhts_bed_multi
BGZF Decompress a Filerduckhts_bgunzip
BGZF Compress a Filerduckhts_bgzip
Detect FASTQ Quality Encodingrduckhts_detect_quality_encoding
Create FASTA Tablerduckhts_fasta
Build FASTA Indexrduckhts_fasta_index
Read multiple FASTA files into a DuckDB tablerduckhts_fasta_multi
Compute FASTA Interval Nucleotide Compositionrduckhts_fasta_nuc
Create FASTQ Tablerduckhts_fastq
Read multiple FASTQ files into a DuckDB tablerduckhts_fastq_multi
List DuckHTS Extension Functionsrduckhts_functions
Create GFF3 Tablerduckhts_gff
Convert GFF3 reader output to Parquet with DuckHTS metadatarduckhts_gff_convert_parquet
Read multiple GFF files into a DuckDB tablerduckhts_gff_multi
Create GTF Tablerduckhts_gtf
Read multiple GTF files into a DuckDB tablerduckhts_gtf_multi
Read HTS Header Metadatarduckhts_hts_header
Read HTS Index Metadatarduckhts_hts_index
Read Raw HTS Index Blobrduckhts_hts_index_raw
Read HTS Index Spansrduckhts_hts_index_spans
Lift Over Variant Coordinates Against a Queryrduckhts_liftover
Load DuckHTS Extensionrduckhts_load
Native mosdepth-Compatible Coverage Outputsrduckhts_mosdepth
Munge Summary Statistics Rowsrduckhts_munge
Create BAM Pileup Tablerduckhts_pileup
samtools idxstats-Compatible Alignment Summaryrduckhts_samtools_idxstats
Compute Polygenic Scoresrduckhts_score
DuckHTS SIMD backend diagnosticsrduckhts_simd_backend rduckhts_simd_backend_available rduckhts_simd_backend_compiled rduckhts_simd_backend_cpu_supported rduckhts_simd_info rduckhts_simd_kernel_info rduckhts_simd_requested_backend rduckhts_simd_set_backend
Create Tabix-Indexed File Tablerduckhts_tabix
Convert generic tabix reader output to Parquet with DuckHTS metadatarduckhts_tabix_convert_parquet
Build Tabix Indexrduckhts_tabix_index
Read multiple tabix-indexed files into a DuckDB tablerduckhts_tabix_multi
Setup HTSlib Environmentsetup_hts_env