Computes samtools coverage-like regional summaries for BAM or CRAM input over a BED target set, with DuckHTS-specific pre/post-filter and strand-aware post-filter outputs.
Usage
rduckhts_bam_bed_coverage(
con,
path,
bed_path,
reference = NULL,
index_path = NULL,
bed_index_path = NULL,
mapq = 0,
min_baseq = 0,
min_read_len = 0,
require_flags = 0,
exclude_flags = 1796,
min_depth = 1,
max_depth = 1e+06,
decompression_threads = 0,
fragment_mode = FALSE,
strand_outputs = TRUE,
processing_threads = 0
)Arguments
- con
A DuckDB connection with DuckHTS loaded
- path
Path to the input BAM or CRAM file
- bed_path
Path to the input BED file
- reference
Optional reference FASTA path for CRAM input when required
- index_path
Optional explicit BAM/CRAM index path
- bed_index_path
Optional explicit BED index path (reserved for future use)
- mapq
Minimum mapping quality threshold for post-filter summaries
- min_baseq
Minimum base quality threshold for post-filter base-level summaries
- min_read_len
Minimum read length threshold for post-filter summaries
- require_flags
Required SAM flag mask
- exclude_flags
Excluded SAM flag mask. Defaults to samtools coverage's `UNMAP|SECONDARY|QCFAIL|DUP` mask.
- min_depth
Minimum depth threshold for covered-base and mean-depth summaries
- max_depth
Maximum per-position depth cap. Set `0` to remove the cap.
- decompression_threads
Integer. Number of htslib decompression worker threads to use for BAM/CRAM input. `0` disables htslib worker threads.
- fragment_mode
Logical. Reserved for future fragment-level semantics.
- strand_outputs
Logical. Emit forward/reverse post-filter summary columns.
- processing_threads
Reserved for future parallel interval processing.