rduckhts_mosdepth: Native mosdepth-Compatible Coverage Outputs
In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

rduckhts_mosdepth

R Documentation

Native mosdepth-Compatible Coverage Outputs

Description

Writes native mosdepth-compatible coverage outputs for indexed BAM or CRAM input.

Usage

rduckhts_mosdepth(
  con,
  prefix,
  path,
  chrom = NULL,
  by = NULL,
  fasta = NULL,
  read_groups = NULL,
  no_per_base = FALSE,
  threads = 2,
  processing_threads = 2,
  flag = 1796,
  include_flag = 0,
  fast_mode = FALSE,
  fragment_mode = FALSE,
  use_median = FALSE,
  mapq = 0,
  min_frag_len = -1,
  max_frag_len = -1,
  precision_digits = 2,
  quantize = NULL,
  thresholds = NULL,
  index_path = NULL,
  overwrite = FALSE
)

Arguments

`con`	A DuckDB connection with DuckHTS loaded
`prefix`	Output prefix for the mosdepth-style files
`path`	Path to the input BAM or CRAM file
`chrom`	Optional chromosome name filter
`by`	Optional fixed-width window size as a string or a BED file path
`fasta`	Optional reference FASTA path for CRAM input when required
`read_groups`	Optional comma-separated read-group IDs, matching mosdepth's '-R'
`no_per_base`	Skip writing '{prefix}.per-base.bed.gz'
`threads`	Number of BAM decompression threads
`processing_threads`	Number of parallel contig processing threads (0 = sequential)
`flag`	Excluded SAM flag mask, matching mosdepth's '-F'
`include_flag`	Required SAM flag mask, matching mosdepth's '-i'
`fast_mode`	Logical. If 'TRUE', use mosdepth fast mode. Defaults to 'FALSE', matching upstream mosdepth.
`fragment_mode`	Logical. If 'TRUE', count full fragment insert spans for proper pairs, matching mosdepth's '-a'. Cannot be combined with 'fast_mode = TRUE'.
`use_median`	Logical. If 'TRUE', write 'by' region values as medians instead of means, matching mosdepth's '-m'.
`mapq`	Minimum mapping quality threshold
`min_frag_len`	Minimum absolute template length to keep, matching mosdepth's '-l'
`max_frag_len`	Maximum absolute template length to keep, matching mosdepth's '-u'
`precision_digits`	Number of decimal places to write in the text outputs
`quantize`	Optional mosdepth-style quantize specification such as '":1:4:"'
`thresholds`	Optional comma-separated coverage thresholds for ‘by', matching mosdepth’s '-T'
`index_path`	Optional explicit BAM index path
`overwrite`	Overwrite existing output files