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