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Build a BAM QC report card

Source: R/qc_report_card.R
bam_qc_report_card.Rd

bam_qc_report_card() evaluates Bamana-derived BAM evidence against pass/warn/fail checks for alignment QC and reporting. It consumes the R-native objects returned by bam_summary(), bam_check_index(), bam_check_sort(), bam_check_tag(), bam_check_eof(), and bam_validate(); it does not call Bamana directly.

Usage

bam_qc_report_card(
  summary = NULL,
  index = NULL,
  mapping = NULL,
  sorting = NULL,
  tags = NULL,
  eof = NULL,
  validation = NULL,
  provenance_anomalies = NULL,
  expected_tags = character(),
  thresholds = bam_qc_report_card_thresholds(),
  schema_version = "flounder.bam_qc_report_card.v1"
)

Arguments

summary

Optional bam_summary() result.

index

Optional bam_check_index() result.

mapping

Optional bam_check_map() result used as a fallback for mapping-fraction evidence when summary is absent.

sorting

Optional bam_check_sort() result.

tags

Optional bam_check_tag() data frame or list of such data frames.

eof

Optional bam_check_eof() data frame.

validation

Optional bam_validate() result.

provenance_anomalies

Optional numeric anomaly count or data frame of provenance findings from a future Bamana provenance/forensic surface.

expected_tags

Character vector of BAM aux tags expected to be present.

thresholds

Named threshold list. Defaults to bam_qc_report_card_thresholds().

schema_version

Schema version label to attach to the returned table.

Value

A tibble using the standard report-card schema: schema_version, check_id, check_label, status, observed_value, warn_threshold, fail_threshold, comparator, and details.

Examples

if (FALSE) { # \dontrun{
bam <- bam_summary("reads.bam")
bam_qc_report_card(summary = bam)
} # }