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Create VCF/BCF Table

Source: R/duckhts.R
rduckhts_bcf.Rd

Creates a DuckDB table from a VCF or BCF file using the DuckHTS extension. This follows the RBCFTools pattern of creating a table that can be queried.

Usage

rduckhts_bcf(
  con,
  table_name,
  path,
  region = NULL,
  index_path = NULL,
  tidy_format = FALSE,
  additional_csq_column_types = NULL,
  scan_mode = NULL,
  decompression_threads = 0,
  decode_error_policy = "null",
  overwrite = FALSE,
  samples = NULL
)

Arguments

con

A DuckDB connection with DuckHTS loaded

table_name

Name for the created table

path

Path to the VCF/BCF file

region

Optional genomic region (e.g., "chr1:1000-2000")

index_path

Optional explicit path to index file (.csi/.tbi)

tidy_format

Logical. If TRUE, FORMAT columns are returned in tidy format

additional_csq_column_types

Optional bcftools-style `PATTERN TYPE` overrides for CSQ/ANN/BCSQ subfield typing, separated by newlines or `;`

scan_mode

Optional scan mode. Use "auto" (default extension behavior) or "sequential" to force full-file streaming instead of index-backed count/parallel scan paths. Sequential mode is incompatible with `region`.

decompression_threads

Integer. Number of htslib decompression worker threads per file handle. Default `0`. Use `0` to keep BCF/VCF reads single-threaded.

decode_error_policy

Character. VCF/BCF decode policy: "null" returns NULL for header-vs-payload type clashes or oversized numeric scalars, "warn" emits a DuckHTS warning and returns NULL, and "error" raises a DuckDB/R error. Missing elements count toward scalar cardinality; vector-end padding does not. A malformed FORMAT tag is withheld for every selected sample on that record. Physical read errors and OOM always fail.

overwrite

Logical. If TRUE, overwrites existing table

samples

Optional HTSlib sample selector: `NULL` or `"-"` keeps all, `""` keeps none, comma-separated names include samples, and a leading `"^"` excludes them. Unknown names error; selected samples retain header order.

Value

Invisible TRUE on success

Examples

library(DBI)
library(duckdb)

con <- rduckhts_connect()
bcf_path <- system.file("extdata", "vcf_file.bcf", package = "Rduckhts")
rduckhts_bcf(con, "variants", bcf_path, overwrite = TRUE)
dbGetQuery(con, "SELECT * FROM variants LIMIT 2")
#>   CHROM     POS   ID REF ALT QUAL FILTER INFO_TEST INFO_DP4 INFO_AC INFO_AN
#> 1     1 3000150 <NA>   C   T 59.2   PASS        NA     NULL       2       4
#> 2     1 3000151 <NA>   C   T 59.2   PASS        NA     NULL       2       4
#>   INFO_INDEL INFO_STR FORMAT_TT_A FORMAT_GT_A FORMAT_GQ_A FORMAT_DP_A
#> 1      FALSE     <NA>        NULL         0/1         245          NA
#> 2      FALSE     <NA>        NULL         0/1         245          32
#>   FORMAT_GL_A FORMAT_TT_B FORMAT_GT_B FORMAT_GQ_B FORMAT_DP_B FORMAT_GL_B
#> 1        NULL        NULL         0/1         245          NA        NULL
#> 2        NULL        NULL         0/1         245          32        NULL
dbDisconnect(con, shutdown = TRUE)