Create SAM/BAM/CRAM Table — rduckhts

Creates a DuckDB table from SAM, BAM, or CRAM files using the DuckHTS extension.

Usage

rduckhts_bam(
  con,
  table_name,
  path,
  region = NULL,
  index_path = NULL,
  reference = NULL,
  standard_tags = FALSE,
  auxiliary_tags = FALSE,
  sequence_encoding = NULL,
  quality_representation = NULL,
  overwrite = FALSE
)

Arguments

con: A DuckDB connection with DuckHTS loaded
table_name: Name for the created table
path: Path to the SAM/BAM/CRAM file
region: Optional genomic region (e.g., "chr1:1000-2000")
index_path: Optional explicit path to index file (.bai/.csi/.crai)
reference: Optional reference file path for CRAM files
standard_tags: Logical. If TRUE, include typed standard SAMtags columns. Default FALSE.
auxiliary_tags: Logical. If TRUE, include AUXILIARY_TAGS map of non-standard tags. Default FALSE.
sequence_encoding: Character. Sequence encoding for the SEQ column: "string" (default) returns decoded bases as VARCHAR; "nt16" returns raw htslib nt16 4-bit codes as UTINYINT[].
quality_representation: Character. Quality representation for the QUAL column: "string" (default) returns canonical Phred+33 text; "phred" returns raw Phred values as UTINYINT[].
overwrite: Logical. If TRUE, overwrites existing table

Value

Invisible TRUE on success

Examples

library(DBI)
library(duckdb)

con <- dbConnect(duckdb::duckdb(config = list(allow_unsigned_extensions = "true")))
rduckhts_load(con)
#> [1] TRUE
bam_path <- system.file("extdata", "range.bam", package = "Rduckhts")
rduckhts_bam(con, "reads", bam_path, overwrite = TRUE)
dbGetQuery(con, "SELECT COUNT(*) FROM reads WHERE FLAG & 4 = 0")
#>   count_star()
#> 1          112
dbDisconnect(con, shutdown = TRUE)