rduckhts_fasta_nuc: Compute FASTA Interval Nucleotide Composition
In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

rduckhts_fasta_nuc

R Documentation

Compute FASTA Interval Nucleotide Composition

Description

Computes bedtools nuc-style nucleotide composition over either a BED file or generated fixed-width bins.

Usage

rduckhts_fasta_nuc(
  con,
  path,
  bed_path = NULL,
  bin_width = NULL,
  region = NULL,
  index_path = NULL,
  gzi_path = NULL,
  bed_index_path = NULL,
  include_seq = FALSE
)

Arguments

`con`	A DuckDB connection with DuckHTS loaded
`path`	Path to the FASTA file
`bed_path`	Optional BED path. Supply exactly one of 'bed_path' or 'bin_width'.
`bin_width`	Optional fixed bin width in base pairs
`region`	Optional FASTA region filter
`index_path`	Optional explicit FASTA index path
`gzi_path`	Optional explicit BGZF FASTA block index path (.gzi) for bgzipped FASTA inputs when the sidecar is not colocated with the FASTA.
`bed_index_path`	Optional explicit BED tabix index path
`include_seq`	Include the fetched interval sequence