fix: correct COI Wright path algorithm — include sire/dam as direct ancestors of each other
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@@ -2,69 +2,102 @@ const express = require('express');
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const router = express.Router();
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const { getDatabase } = require('../db/init');
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// Helper function to calculate inbreeding coefficient
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function calculateCOI(sireId, damId, generations = 5) {
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/**
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* calculateCOI — Wright Path Coefficient method
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*
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* Builds a full ancestor map for BOTH the sire and dam, including
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* themselves at generation 0, so that:
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* - if sire IS a parent of dam (or vice versa), it shows as a
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* common ancestor at gen 0 vs gen 1, giving the correct COI.
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* - multiple paths through the same ancestor are ALL counted.
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*
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* The Wright formula per path: (0.5)^(L+1) * (1 + F_A)
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* where L = number of segregation steps sire-side + dam-side.
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* F_A (inbreeding of common ancestor) is approximated as 0 here.
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*
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* For a direct parent-offspring pair (sire is direct parent of dam):
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* sireGen = 0, damGen = 1 => (0.5)^(0+1+1) = 0.25 => 25% COI
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*/
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function calculateCOI(sireId, damId, generations = 6) {
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const db = getDatabase();
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// Get all ancestors for both parents
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function getAncestors(dogId, currentGen = 0, maxGen = generations) {
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if (currentGen >= maxGen) return [];
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// Returns a list of { id, name, generation } for every ancestor of dogId
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// INCLUDING dogId itself at generation 0.
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function getAncestorMap(dogId) {
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const visited = new Map(); // id -> [{ id, name, generation }, ...]
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const parents = db.prepare(`
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SELECT p.parent_type, p.parent_id, d.name
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FROM parents p
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JOIN dogs d ON p.parent_id = d.id
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WHERE p.dog_id = ?
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`).all(dogId);
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function recurse(id, gen) {
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if (gen > generations) return;
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const ancestors = parents.map(p => ({
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id: p.parent_id,
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name: p.name,
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type: p.parent_type,
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generation: currentGen + 1
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}));
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const dog = db.prepare('SELECT id, name FROM dogs WHERE id = ?').get(id);
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if (!dog) return;
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parents.forEach(p => {
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ancestors.push(...getAncestors(p.parent_id, currentGen + 1, maxGen));
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});
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if (!visited.has(id)) visited.set(id, []);
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visited.get(id).push({ id: dog.id, name: dog.name, generation: gen });
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return ancestors;
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// Only recurse into parents if we haven't already processed this id
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// at this generation (prevents infinite loops on circular data)
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if (visited.get(id).length === 1) {
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const parents = db.prepare(`
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SELECT p.parent_id, d.name
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FROM parents p
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JOIN dogs d ON p.parent_id = d.id
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WHERE p.dog_id = ?
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`).all(id);
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parents.forEach(p => recurse(p.parent_id, gen + 1));
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}
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}
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recurse(dogId, 0);
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return visited;
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}
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const sireAncestors = getAncestors(sireId);
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const damAncestors = getAncestors(damId);
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const sireMap = getAncestorMap(sireId);
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const damMap = getAncestorMap(damId);
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// Find common ancestors
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const commonAncestors = [];
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sireAncestors.forEach(sireAnc => {
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damAncestors.forEach(damAnc => {
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if (sireAnc.id === damAnc.id) {
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commonAncestors.push({
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id: sireAnc.id,
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name: sireAnc.name,
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sireGen: sireAnc.generation,
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damGen: damAnc.generation
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});
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}
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});
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});
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// Find all IDs that appear in BOTH ancestor maps (common ancestors)
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// Exclude the sire and dam themselves from being listed as common ancestors
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// (they can't be common ancestors of the hypothetical offspring with each other)
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const commonIds = [...sireMap.keys()].filter(
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id => damMap.has(id) && id !== parseInt(sireId) && id !== parseInt(damId)
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);
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// Calculate COI using path coefficient method
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let coi = 0;
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const processed = new Set();
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const commonAncestorList = [];
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const processedPaths = new Set();
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commonAncestors.forEach(anc => {
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const key = `${anc.id}-${anc.sireGen}-${anc.damGen}`;
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if (!processed.has(key)) {
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processed.add(key);
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const pathLength = anc.sireGen + anc.damGen;
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coi += Math.pow(0.5, pathLength);
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}
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commonIds.forEach(ancId => {
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const sireOccurrences = sireMap.get(ancId);
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const damOccurrences = damMap.get(ancId);
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// Wright: sum over every combination of paths through this ancestor
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sireOccurrences.forEach(sireOcc => {
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damOccurrences.forEach(damOcc => {
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const pathKey = `${ancId}-${sireOcc.generation}-${damOcc.generation}`;
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if (!processedPaths.has(pathKey)) {
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processedPaths.add(pathKey);
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// L = steps from sire to ancestor + steps from dam to ancestor
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// Wright formula: (0.5)^(L+1) where L = sireGen + damGen
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const L = sireOcc.generation + damOcc.generation;
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coi += Math.pow(0.5, L + 1);
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}
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});
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});
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// Build display list using closest occurrence per side
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const closestSire = sireOccurrences.reduce((a, b) => a.generation < b.generation ? a : b);
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const closestDam = damOccurrences.reduce((a, b) => a.generation < b.generation ? a : b);
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commonAncestorList.push({
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id: ancId,
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name: sireOccurrences[0].name,
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sireGen: closestSire.generation,
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damGen: closestDam.generation
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});
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});
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return {
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coefficient: Math.round(coi * 10000) / 100, // Percentage with 2 decimals
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commonAncestors: [...new Map(commonAncestors.map(a => [a.id, a])).values()]
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coefficient: Math.round(coi * 10000) / 100,
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commonAncestors: commonAncestorList
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};
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}
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@@ -89,22 +122,18 @@ router.get('/:id', (req, res) => {
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`).all(dogId);
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const sire = parents.find(p => p.parent_type === 'sire');
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const dam = parents.find(p => p.parent_type === 'dam');
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const dam = parents.find(p => p.parent_type === 'dam');
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return {
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...dog,
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generation: currentGen,
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sire: sire ? buildTree(sire.parent_id, currentGen + 1) : null,
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dam: dam ? buildTree(dam.parent_id, currentGen + 1) : null
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dam: dam ? buildTree(dam.parent_id, currentGen + 1) : null
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};
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}
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const tree = buildTree(req.params.id);
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if (!tree) {
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return res.status(404).json({ error: 'Dog not found' });
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}
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if (!tree) return res.status(404).json({ error: 'Dog not found' });
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res.json(tree);
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} catch (error) {
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res.status(500).json({ error: error.message });
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@@ -140,11 +169,7 @@ router.get('/:id/descendants', (req, res) => {
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}
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const tree = buildDescendantTree(req.params.id);
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if (!tree) {
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return res.status(404).json({ error: 'Dog not found' });
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}
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if (!tree) return res.status(404).json({ error: 'Dog not found' });
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res.json(tree);
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} catch (error) {
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res.status(500).json({ error: error.message });
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@@ -161,7 +186,6 @@ router.post('/trial-pairing', (req, res) => {
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}
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const db = getDatabase();
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// FIX: use single quotes for string literals — SQLite treats double quotes as identifiers
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const sire = db.prepare("SELECT * FROM dogs WHERE id = ? AND sex = 'male'").get(sire_id);
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const dam = db.prepare("SELECT * FROM dogs WHERE id = ? AND sex = 'female'").get(dam_id);
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@@ -172,11 +196,13 @@ router.post('/trial-pairing', (req, res) => {
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const result = calculateCOI(sire_id, dam_id);
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res.json({
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sire: { id: sire.id, name: sire.name },
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dam: { id: dam.id, name: dam.name },
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coi: result.coefficient,
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sire: { id: sire.id, name: sire.name },
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dam: { id: dam.id, name: dam.name },
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coi: result.coefficient,
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commonAncestors: result.commonAncestors,
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recommendation: result.coefficient < 5 ? 'Low risk' : result.coefficient < 10 ? 'Moderate risk' : 'High risk'
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recommendation: result.coefficient < 5 ? 'Low risk'
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: result.coefficient < 10 ? 'Moderate risk'
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: 'High risk'
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});
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} catch (error) {
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res.status(500).json({ error: error.message });
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