rduckhts_bam_bed_coverage: Native BAM/CRAM BED Regional Coverage Summary
In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

rduckhts_bam_bed_coverage

R Documentation

Native BAM/CRAM BED Regional Coverage Summary

Description

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.