message: docs: add new qc config params to input file section
diff: @@ -12,13 +12,13 @@ Nextclade CLI flag: `--input-fasta`
  Nextalign CLI flag: `--sequences`
  -Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format), plain text (one sequence per line).
  +Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) or plain text (one sequence per line).
  ## Reference (root) sequence
  Viral nucleotide sequence which serves as a reference for alignment and the analysis. Mutations are called relative to the reference sequence. It is expected to be the root of the [reference tree](#reference-tree). The best results are obtained when the reference sequence is a well-known consensus genome, of a very high quality, preferably complete and unambiguous (spans entire genome and has no ambiguous nucleotides).
  -Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format), plain text. The file is expected to contain only 1 sequence.
  +Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) or plain text. The file is expected to contain only 1 sequence.
  Nextclade Web (advanced mode): accepted in "Root sequence" drag & drop box. A remote URL is also accepted in `input-root-sequence` URL parameter.
  @@ -28,11 +28,11 @@ Nextalign CLI flag: ` --reference`
  ## Reference tree
  -The reference phylogenetic tree which serves as a target for phylogenetic placement (see [Algorithm: Phylogenetic placement](algorithm/05-phylogenetic-placement)) and a source of clade information for clade assignment (see [Algorithm: Clade Assignment](algorithm/06-clade-assignment)).
  +The phylogenetic reference tree which serves as a target for phylogenetic placement (see [Algorithm: Phylogenetic placement](algorithm/05-phylogenetic-placement)). Nearest neighbour information is used to assign clades (see [Algorithm: Clade Assignment](algorithm/06-clade-assignment)) and to identify private mutations, including reversions.
  The tree **must** be rooted at the sample that matches the [reference (root) sequence](#reference-root-sequence).
  -The tree **must** contain a clade definition for every node.
  +The tree **must** contain a clade definition for every node (including internal).
  The tree **must** be sufficiently large, diverse and to meet clade assignment expectations of a particular use-case, study or experiment. Only clades present on the reference tree can be assigned to [Query sequences](terminology.html#query-sequence).
  @@ -58,7 +58,13 @@ Accepted formats: JSON. Example configuration for SARS-CoV-2:
  "privateMutations": {
  "enabled": true,
  "typical": 8,
  - "cutoff": 24
  + "cutoff": 24,
  + "weightLabeledSubstitutions": 4,
  + "weightLabeledDeletions": 4,
  + "weightReversionSubstitutions": 6,
  + "weightReversionDeletions": 8,
  + "weightUnlabeledSubstitutions": 1,
  + "weightUnlabeledDeletions": 1
  },
  "missingData": {
  "enabled": true,
  @@ -76,7 +82,11 @@ Accepted formats: JSON. Example configuration for SARS-CoV-2:
  "mixedSitesThreshold": 10
  },
  "frameShifts": {
  - "enabled": true
  + "enabled": true,
  + "ignoredFrameShifts": [
  + { "geneName": "ORF3a", "codonRange": {"begin": 256, "end": 276 } },
  + { "geneName": "ORF3a", "codonRange": {"begin": 258, "end": 276 } },
  + ]
  },
  "stopCodons": {
  "enabled": true,
  