Document the new consequence annotations (bilingual) and changelog

Document the SO Term, Impact, Grantham and MNV Consequence Shift columns
in the English and Spanish output-formats pages, and record the three new
consequence annotations in the changelog.

Author: Paururo

CHANGELOG.md

@@ -5,6 +5,9 @@ All notable changes to this project are documented in this file.
 ## [1.1.5] - 2026-06-09
 
 ### Added
+- **Sequence Ontology consequence terms and impact levels.** New `SO Term` and `Impact` TSV columns (and `SO` / `IMPACT` VCF INFO fields) annotate every variant with a standard SO term (`missense_variant`, `synonymous_variant`, `stop_gained`, `stop_lost`, `start_lost`, `frameshift_variant`, `inframe_insertion`/`inframe_deletion`, `intergenic_variant`, `coding_sequence_variant`) and a `HIGH`/`MODERATE`/`LOW`/`MODIFIER` impact, following SnpEff/VEP conventions.
+- **Grantham distance for missense changes.** A new `Grantham` TSV column (and `GD` VCF INFO field) reports the Grantham (1974) distance of the combined amino-acid substitution together with its conservation category (e.g. `177 (radical)`), for genuine missense changes only.
+- **MNV-vs-SNV consequence shift.** A new `MNV Consequence Shift` TSV column (and `MNVSHIFT` VCF INFO field) flags whether a combined MNV is `MNV-gained` (more severe than any single SNV alone — e.g. two individually-synonymous SNVs producing a non-synonymous residue, which per-SNV annotators miss), `MNV-masked` (a nonsense SNV rescued by its neighbour), or `Concordant`.
 - Added regression coverage for phased MNV-plus-indel haplotypes, verifying that codon MNV rows overlapping an indel are flagged as `Indel overlap` while BAM-supported combined events are emitted as exact `complex_indel` rows.
 - Added an indel/MNV semantics note documenting caller compatibility, boundary rules, current limits, and how exact complex haplotypes are represented.
 - Added transcript-aware regression coverage for exon-junction MNV codons and restored-frame indel contexts in multi-exon CDS models.

docs/output-formats.es.md

@@ -32,6 +32,10 @@ Columnas principales:
 | `MNV Codon` | Codón con todas las sustituciones agrupadas. |
 | `Event Class` | Clase canónica del evento de alelo: `snp`, `mnv`, `insertion`, `deletion`, `delins`, `complex_indel` o `symbolic`. |
 | `Event Components` | Descomposición REF/ALT como `SNV:10:A>G`, `INS:10:+T` o `DEL:11-12:TG`. |
+| `SO Term` | Término de consecuencia Sequence Ontology (`missense_variant`, `synonymous_variant`, `stop_gained`, `start_lost`, `frameshift_variant`, `inframe_deletion`, `intergenic_variant`, …). |
+| `Impact` | Impacto previsto según convenciones SnpEff/VEP: `HIGH`, `MODERATE`, `LOW` o `MODIFIER`. |
+| `Grantham` | Distancia de Grantham y categoría de conservación de un cambio missense (p. ej. `177 (radical)`); `-` si es sinónimo, sin sentido o no codificante. |
+| `MNV Consequence Shift` | Cómo compara el MNV combinado con sus SNV individuales: `MNV-gained` (más severo que cualquier SNV solo — lo que se pierden los anotadores por-SNV), `MNV-masked` (un SNV sin sentido rescatado por su vecino) o `Concordant`. `-` para SNV individuales. |
 
 Columnas adicionales cuando se usa `--bam`:
 

docs/output-formats.md

@@ -32,6 +32,10 @@ Main columns:
 | `MNV Codon` | Codon with all grouped substitutions. |
 | `Event Class` | Canonical allele event class: `snp`, `mnv`, `insertion`, `deletion`, `delins`, `complex_indel`, or `symbolic`. |
 | `Event Components` | REF/ALT decomposition such as `SNV:10:A>G`, `INS:10:+T`, or `DEL:11-12:TG`. |
+| `SO Term` | Sequence Ontology consequence term (`missense_variant`, `synonymous_variant`, `stop_gained`, `start_lost`, `frameshift_variant`, `inframe_deletion`, `intergenic_variant`, …). |
+| `Impact` | Predicted impact following SnpEff/VEP conventions: `HIGH`, `MODERATE`, `LOW` or `MODIFIER`. |
+| `Grantham` | Grantham distance and conservation category of a missense change (e.g. `177 (radical)`); `-` for synonymous, nonsense or non-coding changes. |
+| `MNV Consequence Shift` | How the combined MNV compares with its individual SNVs: `MNV-gained` (more severe than any single SNV — what per-SNV annotators miss), `MNV-masked` (a nonsense SNV rescued by its neighbour) or `Concordant`. `-` for single SNVs. |
 
 Extra columns when `--bam` is used: