Package index • RBCFTools

All functions

annot_tsv_path(): Get Path to annot-tsv Executable
bcf_reader_build(): Build the bcf_reader DuckDB extension
bcf_reader_copy_source(): Copy bcf_reader extension source to a build directory
bcftools_bin_dir(): Get Path to bcftools Binary Directory
bcftools_lib_dir(): Get bcftools Library Directory
bcftools_libs(): Get Linker Flags for bcftools Library
bcftools_path(): Get Path to bcftools Executable
bcftools_plugins_dir(): Get Path to bcftools Plugins Directory
bcftools_tools(): List Available bcftools Scripts
bcftools_version(): Get bcftools Version
bgzip_path(): Get Path to bgzip Executable
ducklake: DuckLake helpers for VCF/BCF ETL
ducklake_attach(): Attach a DuckLake catalog (legacy function)
ducklake_connect_catalog(): Connect to a DuckLake catalog with abstracted backend support
ducklake_create_catalog_secret(): Create a DuckLake catalog secret for database credentials
ducklake_create_s3_secret(): Create or replace an S3 secret for DuckLake
ducklake_current_snapshot(): Get current snapshot ID
ducklake_download_mc(): Download a static MinIO client (mc) binary
ducklake_download_minio(): Download a static MinIO server binary
ducklake_drop_secret(): Drop a DuckLake catalog secret
ducklake_list_files(): List files managed by DuckLake for a table
ducklake_list_secrets(): List existing DuckLake catalog secrets
ducklake_load(): Load the DuckLake extension
ducklake_load_vcf(): Load VCF into DuckLake (ETL + Registration)
ducklake_merge(): Merge/upsert data into a DuckLake table
ducklake_options(): Get DuckLake configuration options
ducklake_parse_connection_string(): Parse DuckLake connection string into components
ducklake_query_snapshot(): Query table at a specific snapshot (time travel)
ducklake_register_parquet(): Register existing Parquet files in a DuckLake table
ducklake_set_commit_message(): Set commit message for current transaction
ducklake_set_option(): Set DuckLake configuration option
ducklake_snapshots(): List DuckLake snapshots
ducklake_update_secret(): Update an existing DuckLake catalog secret
htsfile_path(): Get Path to htsfile Executable
htslib_bin_dir(): Get Path to htslib Binary Directory
htslib_capabilities(): Get htslib Capabilities
htslib_cflags(): Get Compiler Flags for htslib
htslib_feature_string(): Get htslib Feature String
htslib_features(): Get htslib Features Bitfield
htslib_has_feature() HTS_FEATURE_CONFIGURE HTS_FEATURE_PLUGINS HTS_FEATURE_LIBCURL HTS_FEATURE_S3 HTS_FEATURE_GCS HTS_FEATURE_LIBDEFLATE HTS_FEATURE_LZMA HTS_FEATURE_BZIP2 HTS_FEATURE_HTSCODECS: Check for a Specific htslib Feature
htslib_include_dir(): Get htslib Include Directory
htslib_lib_dir(): Get htslib Library Directory
htslib_libs(): Get Linker Flags for htslib
htslib_plugins_dir(): Get Path to htslib Plugins Directory
htslib_tools(): List Available htslib Tools
htslib_version(): Get htslib Version
linking_info(): Get All Linking Information for RBCFTools
parquet_kv_metadata(): Read Parquet key-value metadata
parquet_to_vcf(): Convert Parquet back to VCF/BCF format
print(<vcf_duckdb>): Print method for vcf_duckdb objects
print_makevars_config(): Print Makevars Configuration for LinkingTo
ref_cache_path(): Get Path to ref-cache Executable
setup_hts_env(): Setup Environment for Remote File Access
tabix_path(): Get Path to tabix Executable
vcf_arrow_schema(): Get the Arrow schema for a VCF file
vcf_close_duckdb(): Close a VCF DuckDB connection
vcf_count_duckdb(): Count variants in a VCF/BCF file
vcf_count_per_contig(): Get variant counts per contig using bcftools
vcf_count_variants(): Get number of variants using bcftools
vcf_duckdb: DuckDB VCF/BCF Query Utilities
vcf_duckdb_connect(): Setup DuckDB connection with bcf_reader extension loaded
vcf_get_contig_lengths(): Get contig lengths from VCF/BCF file
vcf_get_contigs(): Get contig names from VCF/BCF file
vcf_has_index(): Check if VCF/BCF file has an index
vcf_header_metadata(): Extract VCF header for Parquet key-value storage
vcf_open_arrow(): Create an Arrow stream from a VCF/BCF file
vcf_open_duckdb(): Open a VCF/BCF file as a DuckDB table or view
vcf_query_arrow(): Query VCF/BCF with DuckDB
vcf_query_duckdb(): Query a VCF/BCF file using DuckDB SQL
vcf_read_vep(): Read VCF with parsed VEP annotations
vcf_samples_duckdb(): List samples in a VCF/BCF file using DuckDB
vcf_schema_duckdb(): Get VCF/BCF schema using DuckDB
vcf_summary_duckdb(): Summary statistics for a VCF/BCF file using DuckDB
vcf_to_arrow(): Read VCF/BCF file into a data frame or list of batches
vcf_to_arrow_ipc(): Write VCF/BCF to Arrow IPC format
vcf_to_parquet_arrow(): Write VCF/BCF to Parquet format
vcf_to_parquet_duckdb(): Export VCF/BCF to Parquet using DuckDB
vcf_to_parquet_duckdb_parallel(): Parallel VCF to Parquet conversion using DuckDB
vcf_to_parquet_parallel_arrow(): Parallel VCF to Parquet conversion
vep_detect_tag(): Detect VEP annotation tag in VCF file
vep_get_schema(): Get VEP annotation schema from VCF header
vep_has_annotation(): Check if VCF has VEP-style annotations
vep_infer_type(): Infer type from VEP field name
vep_list_fields(): List VEP annotation fields in a VCF file
vep_parse_record(): Parse VEP annotation string