fix(phpstan): resolve preg_match offset access errors

src/Chromosome.php

@@ -14,12 +14,15 @@ class Chromosome
     public function __construct(string $value)
     {
         /** Matches human chromosomes with or without "chr" prefix: chr1-chr22, chrX, chrY, chrM, chrMT, or 1-22, X, Y, M, MT. */
-        if (preg_match('/^(chr)?(1[0-9]|[1-9]|2[0-2]|X|Y|M|MT)$/i', $value, $matches) === 0) {
+        if (preg_match('/^(?:chr)?(1[0-9]|[1-9]|2[0-2]|X|Y|M|MT)$/i', $value, $matches) === 0) {
             throw new \InvalidArgumentException("Invalid chromosome: {$value}. Expected format: chr1-chr22, chrX, chrY, chrM, or without chr prefix.");
         }
 
-        $value = strtoupper($matches[2]);
-        $this->value = $value === self::MITOCHONDRIAL_ENSEMBL ? self::MITOCHONDRIAL : $value;
+        assert(isset($matches[1]));
+        $value = strtoupper($matches[1]);
+        $this->value = $value === self::MITOCHONDRIAL_ENSEMBL
+            ? self::MITOCHONDRIAL
+            : $value;
     }
 
     public function value(): string

src/GenomicPosition.php

@@ -23,11 +23,16 @@ public function __construct(Chromosome $chromosome, int $position)
     /** @example GenomicPosition::parse('chr1:123456') */
     public static function parse(string $value): self
     {
-        if (preg_match('/^([^:]+):(g\.|)(\d+)$/', $value, $matches) === 0) {
+        if (preg_match('/^([^:]+):(?:g\.)?(\d+)$/', $value, $matches) === 0) {
             throw new \InvalidArgumentException("Invalid genomic position format: {$value}. Expected format: chr1:123456.");
         }
 
-        return new self(new Chromosome($matches[1]), (int) $matches[3]);
+        assert(isset($matches[1], $matches[2]));
+
+        return new self(
+            new Chromosome($matches[1]),
+            SafeCast::toInt($matches[2])
+        );
     }
 
     public function equals(self $other): bool

src/GenomicRegion.php

@@ -36,14 +36,16 @@ public function __construct(
 
     public static function parse(string $value): self
     {
-        if (preg_match('/^([^:]+):(g\.|)(\d+)(-(\d+)|)$/', $value, $matches) === 0) {
+        if (preg_match('/^([^:]+):(?:g\.)?(\d+)(?:-(\d+))?$/', $value, $matches) === 0) {
             throw new \InvalidArgumentException("Invalid genomic region format: {$value}. Expected format: chr1:123-456.");
         }
 
+        assert(isset($matches[1], $matches[2]));
+
         return new self(
             new Chromosome($matches[1]),
-            (int) $matches[3],
-            (int) ($matches[5] ?? $matches[3])
+            SafeCast::toInt($matches[2]),
+            SafeCast::toInt($matches[3] ?? $matches[2])
         );
     }
 

src/IlluminaRunFolder.php

@@ -94,10 +94,14 @@ public static function parse(string $runFolder): self
     private static function extractFlowcellID(string $flowcellSegment): string
     {
         if (preg_match(self::ZERO_PREFIXED_PATTERN, $flowcellSegment, $matches) === 1) {
+            assert(isset($matches[1]));
+
             return $matches[1];
         }
 
         if (preg_match(self::SIDE_PREFIXED_PATTERN, $flowcellSegment, $matches) === 1) {
+            assert(isset($matches[1]));
+
             return $matches[1];
         }