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Summarise a BAM file for nanopore QC

Source: R/bam.R
bam_summary.Rd

bam_summary() calls the curated ../bamana Rust library in-process and returns R-native tables for QC, review, provenance, and report assembly. The binding is intentionally focused on read-only operational summary evidence: it does not attempt to expose all Bamana commands.

Usage

bam_summary(
  path,
  sample_records = 0L,
  prefer_index = FALSE,
  include_mapq_hist = FALSE,
  include_flags = TRUE,
  allow_incomplete = FALSE
)

Arguments

path

Character scalar. Local BAM file to summarise.

sample_records

Integer scalar. Use 0 for a full-file scan, or a positive value for a bounded evidence scan.

prefer_index

Logical scalar. Prefer index-derived counts where Bamana can use a supported sidecar index.

include_mapq_hist

Logical scalar. Include a MAPQ histogram table.

include_flags

Logical scalar. Include flag-category evidence.

allow_incomplete

Logical scalar. Allow Bamana to return partial evidence for incomplete BGZF/BAM input when supported by the backend.

Value

A named list with data frames including status, evidence, header, counts, fractions, fractions_observed, mapq, mapping, anomalies, flag_categories, references, index_derived, and mapq_histogram.

Examples

if (FALSE) { # \dontrun{
bam_summary("reads.bam")
} # }