message: add missing data criterion to QC
diff: @@ -3,7 +3,7 @@ import type { Base, QCDiagnostics, QCResult, ClusteredSNPs } from './run'
  const TooHighDivergence = 'too high divergence'
  const ClusteredSNPsFlag = 'clustered SNPs'
  const TooManyMixedSites = 'Too many non-ACGT characters'
  -// const MissingData = 'missing data'
  +const MissingData = 'missing data'
  // TODO: verify duplicated numbers in this Set. Probably a typo.
  const knownClusters = new Set([28881, 28881, 28883])
  @@ -69,6 +69,7 @@ export function sequenceQC(
  ): QCResult {
  const divergenceThreshold = 15
  const mixedSitesThreshold = 10
  + const missingDataThreshold = 1000
  const flags: string[] = []
  const totalNumberOfMutations =
  @@ -98,6 +99,11 @@ export function sequenceQC(
  if (totalMixedSites > mixedSitesThreshold) {
  flags.push(TooManyMixedSites)
  }
  +
  + if (nucleotideComposition.N && nucleotideComposition.N > missingDataThreshold) {
  + flags.push(MissingData)
  + }
  +
  const diagnostics: QCDiagnostics = { clusteredSNPs, totalMixedSites, totalNumberOfMutations }
  return { flags, diagnostics, nucleotideComposition }
  }
  