Package: Rduckhts 2.0.2.0.1.1

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], Ryan Ward [aut], Nurture Bio [cph], James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan, Andrew Whitwham,Thomas Keane , Robert M Davies [ctb], DuckHTS Contributors [cph], RBCFTools Authors [cph], Genome Research Ltd [cph], Broad Institute [cph], Massachusetts Institute of Technology [cph], Medical Research Council [cph], Attractive Chaos [cph], Dana-Farber Cancer Institute [cph], Brent Pedersen [cph], Giulio Genovese [cph], GENOMICS plc [cph], Nicola Asuni [cph], Devon Ryan [cph], Stichting DuckDB Foundation [cph]

Rduckhts_2.0.2.0.1.1.tar.gz
Rduckhts_2.0.2.0.1.1.zip(r-4.7-x86_64)Rduckhts_2.0.2.0.1.1.zip(r-4.7-arm64)Rduckhts_2.0.2.0.1.1.zip(r-4.6-x86_64)Rduckhts_2.0.2.0.1.1.zip(r-4.6-arm64)
Rduckhts_2.0.2.0.1.1.tar.gz(r-4.7-arm64)Rduckhts_2.0.2.0.1.1.tar.gz(r-4.7-x86_64)Rduckhts_2.0.2.0.1.1.tar.gz(r-4.6-arm64)Rduckhts_2.0.2.0.1.1.tar.gz(r-4.6-x86_64)
Rduckhts_2.0.2.0.1.1.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://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

On CRAN:

Conda:

2.82 score 2 packages 6 scripts 388 downloads 97 exports 2 dependencies

Last updated from:ec493e250f. Checks:10 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK272
linux-devel-x86_64OK551
source / vignettesOK204
linux-release-arm64OK282
linux-release-x86_64OK310
windows-devel-arm64OK464
windows-devel-x86_64OK369
windows-release-arm64OK423
windows-release-x86_64OK257
wasm-releaseOK127

Exports:detect_complex_typesduckdb_type_mappingsduckhts_bootstrapduckhts_buildduckhts_loadextract_array_elementextract_map_datanormalize_tabix_typesrduckhts_ancestry_bamrduckhts_ancestry_genorduckhts_ancestry_panelrduckhts_ancestry_proportionsrduckhts_bamrduckhts_bam_bed_coveragerduckhts_bam_bin_countsrduckhts_bam_convert_parquetrduckhts_bam_indexrduckhts_bam_insert_size_countsrduckhts_bam_insert_size_counts_sqlrduckhts_bam_mate_overlap_countsrduckhts_bam_mismatch_countsrduckhts_bam_multirduckhts_bcfrduckhts_bcf_convert_parquetrduckhts_bcf_indexrduckhts_bcf_multirduckhts_bcf_samplesrduckhts_bcftools_normrduckhts_bedrduckhts_bed_multirduckhts_bgunziprduckhts_bgziprduckhts_bigwigrduckhts_connectrduckhts_count_error_fitrduckhts_count_mixture_lowpassrduckhts_depth_binsrduckhts_depth_region_fractionrduckhts_depth_sex_fractionrduckhts_depth_state_segmentsrduckhts_depth_state_solutionsrduckhts_detect_quality_encodingrduckhts_fastarduckhts_fasta_indexrduckhts_fasta_multirduckhts_fasta_nucrduckhts_fastqrduckhts_fastq_multirduckhts_functionsrduckhts_genbankrduckhts_genbank_to_fastarduckhts_genorduckhts_geno_sitesrduckhts_gffrduckhts_gff_convert_parquetrduckhts_gff_multirduckhts_gtfrduckhts_gtf_multirduckhts_hts_headerrduckhts_hts_indexrduckhts_hts_index_rawrduckhts_hts_index_spansrduckhts_htslib_configrduckhts_htslib_inforduckhts_htslib_versionrduckhts_install_macrosrduckhts_liftoverrduckhts_loadrduckhts_mosdepthrduckhts_mungerduckhts_pileuprduckhts_rohrduckhts_roh_countsrduckhts_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_somalier_bam_countsrduckhts_somalier_charrrduckhts_somalier_find_sitesrduckhts_somalier_import_sitesrduckhts_somalier_matched_contaminationrduckhts_somalier_relatednessrduckhts_somalier_sexrduckhts_somalier_sketchesrduckhts_somalier_vcf_countsrduckhts_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
Retired manual DuckHTS extension builderduckhts_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
Project ancestry directly from an indexed BAM or CRAMrduckhts_ancestry_bam
Estimate ancestry from a materialized `read_geno` relationrduckhts_ancestry_geno
Create a deterministic ancestry site panel for BAM/CRAM countsrduckhts_ancestry_panel
Estimate projected ancestry proportions from frequency or dosage relationsrduckhts_ancestry_proportions
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
BAM/CRAM Insert-Size Countsrduckhts_bam_insert_size_counts rduckhts_bam_insert_size_counts_sql
Count Agreement Between Overlapping Matesrduckhts_bam_mate_overlap_counts
Count Aligned Bases Against the Referencerduckhts_bam_mismatch_counts
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
Read the VCF/BCF Sample Catalogrduckhts_bcf_samples
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
Create a BigWig Signal Tablerduckhts_bigwig
Create a DuckDB connection with bundled DuckHTS loadedrduckhts_connect
Fit Read Error and Contamination from Allele Read Countsrduckhts_count_error_fit
Estimate a Conditional Second-Genome Share from Low-Pass Countsrduckhts_count_mixture_lowpass
Correct Bin Read Counts for GC Contentrduckhts_depth_bins
Estimate the Share of Cells with a One-Copy Change of a Regionrduckhts_depth_region_fraction
Estimate the Share of a Second Genome of the Other Sex from X and Y Depthrduckhts_depth_sex_fraction
Decode Tumour Fraction, Ploidy and Copy-Number Segments from Corrected Binsrduckhts_depth_state_segments rduckhts_depth_state_solutions
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 GenBank Feature Tablerduckhts_genbank
Write GenBank Sequence as FASTArduckhts_genbank_to_fasta
Read Record-Major Genotypesrduckhts_geno
Fetch Exact Alleles at Requested Sitesrduckhts_geno_sites
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
Get the Installed htslib Linking Contractrduckhts_htslib_config
Inspect the Loaded htslib Buildrduckhts_htslib_info
Return the Loaded htslib Versionrduckhts_htslib_version
Install DuckHTS macros on a connectionrduckhts_install_macros
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
Find Runs of Homozygosityrduckhts_roh
Find Runs of Homozygosity from Read Countsrduckhts_roh_counts
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
Extract Panel-Aligned Counts from BAM or CRAMrduckhts_somalier_bam_counts
Estimate Per-Sample Contamination with CHARRrduckhts_somalier_charr
Select a Somalier Panel from Population Variantsrduckhts_somalier_find_sites
Import an Already Selected Somalier Sites VCF or BCFrduckhts_somalier_import_sites
Estimate Directional Contamination Against Matched Anchorsrduckhts_somalier_matched_contamination
Compare Somalier-Derived Sample Sketchesrduckhts_somalier_relatedness
Infer X/Y Dosage Sex Evidencerduckhts_somalier_sex
Prepare Somalier-Derived Sample Sketchesrduckhts_somalier_sketches
Extract Panel-Aligned Counts from VCF or BCFrduckhts_somalier_vcf_counts
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