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Check BAM aux-tag evidence for library/QC review

Source: R/bam.R
bam_check_tag.Rd

bam_check_tag() calls Bamana's in-process Rust aux-tag check. It is useful for QC report cards that need bounded or full-scan evidence for tags such as read groups, molecular identifiers, or alignment annotations.

Usage

bam_check_tag(
  path,
  tag,
  sample_records = 1000L,
  full_scan = FALSE,
  require_type = NULL,
  count_hits = FALSE
)

Arguments

path

Character scalar. Local BAM file to inspect.

tag

Character scalar. Two-character BAM aux tag to search for.

sample_records

Integer scalar. Number of records to examine when full_scan = FALSE; use 0 only with full_scan = TRUE.

full_scan

Logical scalar. Scan the full file for absence/presence evidence.

require_type

Optional character scalar. Bamana aux type code to require, for example "Z" or "i".

count_hits

Logical scalar. Count all matching records during the scan.

Value

A one-row data frame with tag evidence, mode, confidence, and Bamana error metadata columns.

Examples

if (FALSE) { # \dontrun{
bam_check_tag("reads.bam", "RG", full_scan = TRUE)
} # }