feat: Add ClusterOverlapCalculator for efficient S

src/Snps/Analysis/ClusterOverlapCalculator.php

@@ -0,0 +1,32 @@
+<?php
+
+namespace Dna\Snps\Analysis;
+
+class ClusterOverlapCalculator
+{
+    public function computeClusterOverlap(array $snps, array $chipClusters, float $clusterOverlapThreshold = 0.95): array
+    {
+        $overlapResults = [];
+        foreach ($chipClusters as $clusterId => $clusterData) {
+            $snpsInCluster = array_filter($snps, function ($snp) use ($clusterData) {
+                return in_array($snp['chrom'], $clusterData['chromosomes']) && $snp['pos'] >= $clusterData['start'] && $snp['pos'] <= $clusterData['end'];
+            });
+
+            $snpsInCommon = count($snpsInCluster);
+            $totalSnpsInCluster = count($clusterData['snps']);
+            $overlapWithCluster = $snpsInCommon / $totalSnpsInCluster;
+            $overlapWithSelf = $snpsInCommon / count($snps);
+
+            if ($overlapWithCluster > $clusterOverlapThreshold && $overlapWithSelf > $clusterOverlapThreshold) {
+                $overlapResults[$clusterId] = [
+                    'overlapWithCluster' => $overlapWithCluster,
+                    'overlapWithSelf' => $overlapWithSelf,
+                    'snpsInCommon' => $snpsInCommon,
+                    'totalSnpsInCluster' => $totalSnpsInCluster,
+                ];
+            }
+        }
+
+        return $overlapResults;
+    }
+}