Convert BAM/CRAM to WisecondorX NPZ format (upstream CLI wrapper)

Calls wisecondorx convert via condathis::run() to convert an aligned BAM or CRAM file to a .npz file for downstream use with wisecondorx_newref() or wisecondorx_predict().

Usage

wisecondorx_convert(
  bam,
  npz,
  reference = NULL,
  binsize = 5000L,
  normdup = FALSE,
  env_name = "wisecondorx",
  extra_args = character(0)
)

Arguments

bam: Path to an indexed BAM or CRAM file.
npz: Path for the output .npz file (created or overwritten).
reference: Optional path to a FASTA reference file. Required when bam is a CRAM file. Passed to upstream --reference.
binsize: Bin size in base pairs (default 5000). The reference bin size should be a multiple of this value. Passed to upstream --binsize.
normdup: Logical; when TRUE, passes --normdup to skip duplicate removal. Recommended for NIPT data where read depth is low.
env_name: Name of the conda environment containing wisecondorx (default "wisecondorx"). Created automatically by condathis on first use via the bioconda channel.
extra_args: Character vector of additional arguments passed verbatim after the mapped CLI flags. For forward compatibility with future upstream WisecondorX releases.

Value

npz (invisibly).

Details

This wrapper exposes the upstream wisecondorx convert CLI flags: --reference, --binsize, and --normdup.

For a fully native R implementation (no Python dependency) that uses Rduckhts instead of pysam, see bam_convert() and bam_convert_npz().

Examples

if (FALSE) { # \dontrun{
wisecondorx_convert(
  bam = "sample.bam",
  npz = "sample.npz",
  binsize = 5000L,
  normdup = FALSE
)
} # }