Package: RBCFTools 1.23-0.0.3.1.9001

Sounkou Mahamane Toure

RBCFTools: 'BCFTools', 'libbcftools' and 'htslib' Wrappers and 'BCF'/'VCF' to 'Parquet' Convertors

Bundles the 'htslib' and 'bcftools' libraries and command lines tools for reading and manipulating VCF/BCF files. Includes streaming facilities from VCF to Apache Arrow via 'nanoarrow', enabling export to Arrow IPC format and Parquet format using 'duckdb' including a 'bcf_reader' extension. Utilities for reading and writing VCF/BCF files into 'DuckLake' are included. provided.

Authors:Sounkou Mahamane Toure [aut, cre], Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas Davies, Robert M, Pierre Lindenbaum [cph], Zilong Li [cph], Duckdb C API and extension and API authors [cph], Giulio Genovese [cph]

RBCFTools_1.23-0.0.3.1.9001.tar.gz

RBCFTools_1.23-0.0.3.1.9001.tgz(r-4.6-x86_64)RBCFTools_1.23-0.0.3.1.9001.tgz(r-4.6-arm64)RBCFTools_1.23-0.0.3.1.9001.tgz(r-4.5-x86_64)RBCFTools_1.23-0.0.3.1.9001.tgz(r-4.5-arm64)
RBCFTools_1.23-0.0.3.1.9001.tar.gz(r-4.7-arm64)RBCFTools_1.23-0.0.3.1.9001.tar.gz(r-4.7-x86_64)RBCFTools_1.23-0.0.3.1.9001.tar.gz(r-4.6-arm64)RBCFTools_1.23-0.0.3.1.9001.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RBCFTools/json (API)

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

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

Pkgdown/docs site:https://rgenomicsetl.github.io

On CRAN:

Conda:

bcftoolsduckdbducklakegenomicshtslibnanoarrowparquet

3.19 score 2 stars 22 scripts 91 exports 6 dependencies

Last updated from:6ee59bc75a. Checks:10 OK, 2 NOTE, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK331
linux-devel-x86_64OK255
source / vignettesOK392
linux-release-arm64OK331
linux-release-x86_64OK377
macos-release-arm64OK169
macos-release-x86_64OK424
macos-oldrel-arm64NOTE235
macos-oldrel-x86_64NOTE368
windows-develOK87
windows-releaseOK98
windows-oldrelOK71
wasm-releaseFAIL247

Exports:annot_tsv_pathbcf_reader_buildbcf_reader_copy_sourcebcftools_bin_dirbcftools_lib_dirbcftools_libsbcftools_pathbcftools_plugins_dirbcftools_toolsbcftools_versionbgzip_pathducklake_attachducklake_connect_catalogducklake_create_catalog_secretducklake_create_s3_secretducklake_current_snapshotducklake_download_mcducklake_download_minioducklake_drop_secretducklake_list_filesducklake_list_secretsducklake_loadducklake_load_vcfducklake_mergeducklake_optionsducklake_parse_connection_stringducklake_query_snapshotducklake_register_parquetducklake_set_commit_messageducklake_set_optionducklake_snapshotsducklake_update_secretHTS_FEATURE_BZIP2HTS_FEATURE_CONFIGUREHTS_FEATURE_GCSHTS_FEATURE_HTSCODECSHTS_FEATURE_LIBCURLHTS_FEATURE_LIBDEFLATEHTS_FEATURE_LZMAHTS_FEATURE_PLUGINSHTS_FEATURE_S3htsfile_pathhtslib_bin_dirhtslib_capabilitieshtslib_cflagshtslib_feature_stringhtslib_featureshtslib_has_featurehtslib_include_dirhtslib_lib_dirhtslib_libshtslib_plugins_dirhtslib_toolshtslib_versionlinking_infoparquet_kv_metadataparquet_to_vcfprint_makevars_configref_cache_pathsetup_hts_envtabix_pathvcf_arrow_schemavcf_close_duckdbvcf_count_duckdbvcf_count_per_contigvcf_count_variantsvcf_duckdb_connectvcf_get_contig_lengthsvcf_get_contigsvcf_has_indexvcf_header_metadatavcf_open_arrowvcf_open_duckdbvcf_query_arrowvcf_query_duckdbvcf_read_vepvcf_samples_duckdbvcf_schema_duckdbvcf_summary_duckdbvcf_to_arrowvcf_to_arrow_ipcvcf_to_parquet_arrowvcf_to_parquet_duckdbvcf_to_parquet_duckdb_parallelvcf_to_parquet_parallel_arrowvep_detect_tagvep_get_schemavep_has_annotationvep_infer_typevep_list_fieldsvep_parse_record

Dependencies:cligluelifecyclenanoarrowrlangvctrs

Readme and manuals

Help Manual

Help pageTopics
Get Path to annot-tsv Executableannot_tsv_path
Build the bcf_reader DuckDB extensionbcf_reader_build
Copy bcf_reader extension source to a build directorybcf_reader_copy_source
Get Path to bcftools Binary Directorybcftools_bin_dir
Get bcftools Library Directorybcftools_lib_dir
Get Linker Flags for bcftools Librarybcftools_libs
Get Path to bcftools Executablebcftools_path
Get Path to bcftools Plugins Directorybcftools_plugins_dir
List Available bcftools Scriptsbcftools_tools
Get bcftools Versionbcftools_version
Get Path to bgzip Executablebgzip_path
DuckLake helpers for VCF/BCF ETLducklake
Attach a DuckLake catalog (legacy function)ducklake_attach
Connect to a DuckLake catalog with abstracted backend supportducklake_connect_catalog
Create a DuckLake catalog secret for database credentialsducklake_create_catalog_secret
Create or replace an S3 secret for DuckLakeducklake_create_s3_secret
Get current snapshot IDducklake_current_snapshot
Download a static MinIO client (mc) binaryducklake_download_mc
Download a static MinIO server binaryducklake_download_minio
Drop a DuckLake catalog secretducklake_drop_secret
List files managed by DuckLake for a tableducklake_list_files
List existing DuckLake catalog secretsducklake_list_secrets
Load the DuckLake extensionducklake_load
Load VCF into DuckLake (ETL + Registration)ducklake_load_vcf
Merge/upsert data into a DuckLake tableducklake_merge
Get DuckLake configuration optionsducklake_options
Parse DuckLake connection string into componentsducklake_parse_connection_string
Query table at a specific snapshot (time travel)ducklake_query_snapshot
Register existing Parquet files in a DuckLake tableducklake_register_parquet
Set commit message for current transactionducklake_set_commit_message
Set DuckLake configuration optionducklake_set_option
List DuckLake snapshotsducklake_snapshots
Update an existing DuckLake catalog secretducklake_update_secret
Get Path to htsfile Executablehtsfile_path
Get Path to htslib Binary Directoryhtslib_bin_dir
Get htslib Capabilitieshtslib_capabilities
Get Compiler Flags for htslibhtslib_cflags
Get htslib Feature Stringhtslib_feature_string
Get htslib Features Bitfieldhtslib_features
Check for a Specific htslib Featurehtslib_has_feature HTS_FEATURE_BZIP2 HTS_FEATURE_CONFIGURE HTS_FEATURE_GCS HTS_FEATURE_HTSCODECS HTS_FEATURE_LIBCURL HTS_FEATURE_LIBDEFLATE HTS_FEATURE_LZMA HTS_FEATURE_PLUGINS HTS_FEATURE_S3
Get htslib Include Directoryhtslib_include_dir
Get htslib Library Directoryhtslib_lib_dir
Get Linker Flags for htslibhtslib_libs
Get Path to htslib Plugins Directoryhtslib_plugins_dir
List Available htslib Toolshtslib_tools
Get htslib Versionhtslib_version
Get All Linking Information for RBCFToolslinking_info
Read Parquet key-value metadataparquet_kv_metadata
Convert Parquet back to VCF/BCF formatparquet_to_vcf
Print Makevars Configuration for LinkingToprint_makevars_config
Print method for vcf_duckdb objectsprint.vcf_duckdb
Get Path to ref-cache Executableref_cache_path
Setup Environment for Remote File Accesssetup_hts_env
Get Path to tabix Executabletabix_path
Get the Arrow schema for a VCF filevcf_arrow_schema
Close a VCF DuckDB connectionvcf_close_duckdb
Count variants in a VCF/BCF filevcf_count_duckdb
Get variant counts per contig using bcftoolsvcf_count_per_contig
Get number of variants using bcftoolsvcf_count_variants
DuckDB VCF/BCF Query Utilitiesvcf_duckdb
Setup DuckDB connection with bcf_reader extension loadedvcf_duckdb_connect
Get contig lengths from VCF/BCF filevcf_get_contig_lengths
Get contig names from VCF/BCF filevcf_get_contigs
Check if VCF/BCF file has an indexvcf_has_index
Extract VCF header for Parquet key-value storagevcf_header_metadata
Create an Arrow stream from a VCF/BCF filevcf_open_arrow
Open a VCF/BCF file as a DuckDB table or viewvcf_open_duckdb
Query VCF/BCF with DuckDBvcf_query_arrow
Query a VCF/BCF file using DuckDB SQLvcf_query_duckdb
Read VCF with parsed VEP annotationsvcf_read_vep
List samples in a VCF/BCF file using DuckDBvcf_samples_duckdb
Get VCF/BCF schema using DuckDBvcf_schema_duckdb
Summary statistics for a VCF/BCF file using DuckDBvcf_summary_duckdb
Read VCF/BCF file into a data frame or list of batchesvcf_to_arrow
Write VCF/BCF to Arrow IPC formatvcf_to_arrow_ipc
Write VCF/BCF to Parquet formatvcf_to_parquet_arrow
Export VCF/BCF to Parquet using DuckDBvcf_to_parquet_duckdb
Parallel VCF to Parquet conversion using DuckDBvcf_to_parquet_duckdb_parallel
Parallel VCF to Parquet conversionvcf_to_parquet_parallel_arrow
Detect VEP annotation tag in VCF filevep_detect_tag
Get VEP annotation schema from VCF headervep_get_schema
Check if VCF has VEP-style annotationsvep_has_annotation
Infer type from VEP field namevep_infer_type
List VEP annotation fields in a VCF filevep_list_fields
Parse VEP annotation stringvep_parse_record