feat: Implement ReferenceSequenceManager for manag

src/Snps/ReferenceSequenceManager.php

@@ -0,0 +1,66 @@
+<?php
+
+namespace Dna\Snps;
+
+use Dna\Snps\ReferenceSequence;
+
+class ReferenceSequenceManager
+{
+    private array $_reference_sequences = [];
+    private array $validAssemblies = ["NCBI36", "GRCh37", "GRCh38"];
+
+    public function __construct()
+    {
+        $this->init_resource_attributes();
+    }
+
+    private function init_resource_attributes(): void
+    {
+        $this->_reference_sequences = [];
+    }
+
+    public function getReferenceSequences(string $assembly = "GRCh37", array $chroms = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y", "MT"]): array
+    {
+        if (!in_array($assembly, $this->validAssemblies)) {
+            error_log("Invalid assembly");
+            return [];
+        }
+
+        if (!$this->referenceChromsAvailable($assembly, $chroms)) {
+            // Placeholder for logic to fetch paths and URLs for reference sequences
+            $urls = [];
+            $paths = [];
+            $this->_reference_sequences[$assembly] = $this->createReferenceSequences($assembly, $chroms, $urls, $paths);
+        }
+
+        return $this->_reference_sequences[$assembly];
+    }
+
+    private function referenceChromsAvailable(string $assembly, array $chroms): bool
+    {
+        // Placeholder for actual availability check logic
+        return false;
+    }
+
+    protected function createReferenceSequences(string $assembly, array $chroms, array $urls, array $paths): array
+    {
+        $seqs = [];
+
+        foreach ($paths as $i => $path) {
+            if (!$path) {
+                continue;
+            }
+
+            $seqs[$chroms[$i]] = new ReferenceSequence(
+                $chroms[$i],
+                $urls[$i],
+                realpath($path),
+                $assembly,
+                "Homo sapiens",
+                "x"
+            );
+        }
+
+        return $seqs;
+    }
+}