Skip to contents

Validate BAM structure and selected consistency checks

Source: R/bam.R
bam_validate.Rd

bam_validate() calls Bamana's structural validation library path in-process. Validation findings are returned as evidence tables even when Bamana reports validation failure; missing or unreadable inputs without a validation payload still raise typed Bamana-backed R conditions.

Usage

bam_validate(
  path,
  max_errors = 100L,
  max_warnings = 100L,
  header_only = FALSE,
  records = NULL,
  fail_fast = FALSE,
  include_warnings = TRUE
)

Arguments

path

Character scalar. Local BAM file to validate.

max_errors

Positive integer scalar. Maximum error findings to retain.

max_warnings

Non-negative integer scalar. Maximum warning findings to retain.

header_only

Logical scalar. Validate the header only.

records

Optional positive integer scalar. Validate at most this many records after the header.

fail_fast

Logical scalar. Stop at the first error-level finding.

include_warnings

Logical scalar. Include warning-level findings.

Value

A named list with status, summary, findings, and error data frames. status$ok preserves Bamana's command envelope result; a validation failure with findings therefore returns ok = FALSE rather than raising an R error.

Examples

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