From 9aeaf12629b5f7f1c74a0bc0c57126942e782fc0 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 10:58:00 +0200
Subject: [PATCH 01/25] feat: implement interop

---
 src/InterOp/ClusterStatistic.php     |  26 ++
 src/InterOp/DeviationValue.php       |  34 +++
 src/InterOp/InterOpException.php     |   5 +
 src/InterOp/InterOpResult.php        |  73 ++++++
 src/InterOp/LaneResult.php           | 120 +++++++++
 tests/GenomicRegionTest.php          |   2 +-
 tests/InterOp/DeviationValueTest.php |  36 +++
 tests/InterOp/InterOpResultTest.php  |  69 +++++
 tests/InterOp/meta-info-i100.json    | 256 +++++++++++++++++++
 tests/InterOp/meta-info-miseq.json   | 360 +++++++++++++++++++++++++++
 10 files changed, 980 insertions(+), 1 deletion(-)
 create mode 100644 src/InterOp/ClusterStatistic.php
 create mode 100644 src/InterOp/DeviationValue.php
 create mode 100644 src/InterOp/InterOpException.php
 create mode 100644 src/InterOp/InterOpResult.php
 create mode 100644 src/InterOp/LaneResult.php
 create mode 100644 tests/InterOp/DeviationValueTest.php
 create mode 100644 tests/InterOp/InterOpResultTest.php
 create mode 100644 tests/InterOp/meta-info-i100.json
 create mode 100644 tests/InterOp/meta-info-miseq.json

diff --git a/src/InterOp/ClusterStatistic.php b/src/InterOp/ClusterStatistic.php
new file mode 100644
index 0000000..2876f51
--- /dev/null
+++ b/src/InterOp/ClusterStatistic.php
@@ -0,0 +1,26 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+class ClusterStatistic
+{
+    /** @var DeviationValue Cluster density (K/mm²). */
+    public $density;
+
+    /** @var DeviationValue Percentage of clusters passing filter. */
+    public $clusterPF;
+
+    /** @var float Total cluster count (millions). */
+    public $clusterCount;
+
+    /** @var float Clusters passing filter (millions). */
+    public $clusterCountPF;
+
+    public function __construct(DeviationValue $density, DeviationValue $clusterPF, float $clusterCount, float $clusterCountPF)
+    {
+        $this->density = $density;
+        $this->clusterPF = $clusterPF;
+        $this->clusterCount = $clusterCount;
+        $this->clusterCountPF = $clusterCountPF;
+    }
+}
diff --git a/src/InterOp/DeviationValue.php b/src/InterOp/DeviationValue.php
new file mode 100644
index 0000000..0167d2c
--- /dev/null
+++ b/src/InterOp/DeviationValue.php
@@ -0,0 +1,34 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+use function Safe\preg_match;
+
+class DeviationValue
+{
+    /** @var float */
+    public $value;
+
+    /** @var float */
+    public $deviation;
+
+    public function __construct(float $value, float $deviation)
+    {
+        $this->value = $value;
+        $this->deviation = $deviation;
+    }
+
+    /**
+     * Parses strings like "851 +/- 32" into value and deviation.
+     *
+     * Returns null for "nan +/- nan" (occurs for index reads).
+     */
+    public static function parse(string $raw): ?self
+    {
+        if (preg_match('/^([\d.]+)\s*\+\/-\s*([\d.]+)$/', $raw, $matches) !== 1) {
+            return null;
+        }
+
+        return new self((float) $matches[1], (float) $matches[2]);
+    }
+}
diff --git a/src/InterOp/InterOpException.php b/src/InterOp/InterOpException.php
new file mode 100644
index 0000000..d0a90be
--- /dev/null
+++ b/src/InterOp/InterOpException.php
@@ -0,0 +1,5 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+class InterOpException extends \Exception {}
diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
new file mode 100644
index 0000000..e697441
--- /dev/null
+++ b/src/InterOp/InterOpResult.php
@@ -0,0 +1,73 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+class InterOpResult
+{
+    /** @var LaneResult */
+    public $resultsForRead1;
+
+    /** @var LaneResult */
+    public $resultsForRead2;
+
+    /** @var RunResult */
+    public $resultsForRun;
+
+    /**
+     * @param array<int, array<string, string>> $summary interop summary rows
+     * @param array<string, array<int, array<string, string>>> $reads interop reads keyed by read name
+     */
+    public function __construct(array $summary, array $reads)
+    {
+        [$firstDataRead, $lastDataRead] = self::findDataReads($summary);
+
+        $read1Rows = $reads[$firstDataRead] ?? null;
+        if ($read1Rows === null) {
+            throw new InterOpException("Reads data missing for '{$firstDataRead}'.");
+        }
+
+        $read2Rows = $reads[$lastDataRead] ?? null;
+        if ($read2Rows === null) {
+            throw new InterOpException("Reads data missing for '{$lastDataRead}'.");
+        }
+
+        $this->resultsForRead1 = LaneResult::fromInterOpRow($read1Rows[0]);
+        $this->resultsForRead2 = LaneResult::fromInterOpRow($read2Rows[0]);
+        $this->resultsForRun = RunResult::fromLaneResults($this->resultsForRead1, $this->resultsForRead2);
+    }
+
+    /**
+     * Finds the first and last data (non-index) reads from summary entries.
+     *
+     * Index reads have "(I)" suffix in their Level field (e.g. "Read 2 (I)").
+     * Data reads lack this suffix. The first and last non-index entries are the
+     * two data reads, regardless of device type:
+     * - MiSeq single-index: Read 1, Read 3
+     * - MiSeq dual-index: Read 1, Read 4
+     * - i100: Read 3, Read 4
+     *
+     * @param array<int, array<string, string>> $summary
+     *
+     * @return array{0: string, 1: string}
+     */
+    public static function findDataReads(array $summary): array
+    {
+        $dataReads = [];
+        foreach ($summary as $entry) {
+            $level = $entry['Level'];
+            if ($level === 'Non-indexed' || $level === 'Total') {
+                continue;
+            }
+
+            if (substr($level, -3) !== '(I)') {
+                $dataReads[] = $level;
+            }
+        }
+
+        if (count($dataReads) < 2) {
+            throw new InterOpException('Expected at least 2 data reads, found ' . count($dataReads) . '.');
+        }
+
+        return [$dataReads[0], $dataReads[count($dataReads) - 1]];
+    }
+}
diff --git a/src/InterOp/LaneResult.php b/src/InterOp/LaneResult.php
new file mode 100644
index 0000000..08b8c7d
--- /dev/null
+++ b/src/InterOp/LaneResult.php
@@ -0,0 +1,120 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+class LaneResult
+{
+    /** @var ClusterStatistic */
+    public $clusterStatistic;
+
+    /** @var SequencingQualityControl */
+    public $sequencingQualityControl;
+
+    /** @var int Intensity at cycle 1. */
+    public $intensityCycle;
+
+    /** @var int Yield in bases (JSON float in gigabases * 1_000_000). */
+    public $yield;
+
+    public function __construct(ClusterStatistic $clusterStatistic, SequencingQualityControl $sequencingQualityControl, int $intensityCycle, int $yield)
+    {
+        $this->clusterStatistic = $clusterStatistic;
+        $this->sequencingQualityControl = $sequencingQualityControl;
+        $this->intensityCycle = $intensityCycle;
+        $this->yield = $yield;
+    }
+
+    /**
+     * Builds a LaneResult from the first row (Surface "-") of a reads entry.
+     *
+     * @param array<string, string> $row single lane row from interop reads data
+     */
+    public static function fromInterOpRow(array $row): self
+    {
+        $density = DeviationValue::parse($row['Density']);
+        assert($density instanceof DeviationValue, "Expected parseable Density, got: {$row['Density']}");
+
+        $clusterPF = DeviationValue::parse($row['Cluster PF']);
+        assert($clusterPF instanceof DeviationValue, "Expected parseable Cluster PF, got: {$row['Cluster PF']}");
+
+        $aligned = DeviationValue::parse($row['Aligned']);
+        assert($aligned instanceof DeviationValue, "Expected parseable Aligned, got: {$row['Aligned']}");
+
+        $error = DeviationValue::parse($row['Error']);
+        assert($error instanceof DeviationValue, "Expected parseable Error, got: {$row['Error']}");
+
+        $intensityCycle = DeviationValue::parse($row['Intensity C1']);
+        assert($intensityCycle instanceof DeviationValue, "Expected parseable Intensity C1, got: {$row['Intensity C1']}");
+
+        $phasingParts = explode(' / ', $row['Legacy Phasing/Prephasing Rate']);
+        assert(count($phasingParts) === 2, "Expected 'phasing / prephasing' format, got: {$row['Legacy Phasing/Prephasing Rate']}");
+        assert($phasingParts[0] !== 'nan', 'Unexpected nan phasing rate for data read');
+
+        $clusterStatistic = new ClusterStatistic(
+            $density,
+            $clusterPF,
+            (float) $row['Reads'],
+            (float) $row['Reads PF']
+        );
+
+        $sequencingQualityControl = new SequencingQualityControl(
+            (float) $row['%>=Q30'],
+            (float) $phasingParts[0],
+            (float) $phasingParts[1],
+            $aligned,
+            $error
+        );
+
+        return new self(
+            $clusterStatistic,
+            $sequencingQualityControl,
+            (int) $intensityCycle->value,
+            (int) ((float) $row['Yield'] * 1000000)
+        );
+    }
+
+    public static function aggregate(self $a, self $b): self
+    {
+        $density = new DeviationValue(
+            ($a->clusterStatistic->density->value + $b->clusterStatistic->density->value) / 2,
+            ($a->clusterStatistic->density->deviation + $b->clusterStatistic->density->deviation) / 2
+        );
+
+        $clusterPF = new DeviationValue(
+            ($a->clusterStatistic->clusterPF->value + $b->clusterStatistic->clusterPF->value) / 2,
+            ($a->clusterStatistic->clusterPF->deviation + $b->clusterStatistic->clusterPF->deviation) / 2
+        );
+
+        $clusterStatistic = new ClusterStatistic(
+            $density,
+            $clusterPF,
+            $a->clusterStatistic->clusterCount + $b->clusterStatistic->clusterCount,
+            $a->clusterStatistic->clusterCountPF + $b->clusterStatistic->clusterCountPF
+        );
+
+        $aligned = new DeviationValue(
+            ($a->sequencingQualityControl->aligned->value + $b->sequencingQualityControl->aligned->value) / 2,
+            ($a->sequencingQualityControl->aligned->deviation + $b->sequencingQualityControl->aligned->deviation) / 2
+        );
+
+        $error = new DeviationValue(
+            ($a->sequencingQualityControl->error->value + $b->sequencingQualityControl->error->value) / 2,
+            ($a->sequencingQualityControl->error->deviation + $b->sequencingQualityControl->error->deviation) / 2
+        );
+
+        $sequencingQualityControl = new SequencingQualityControl(
+            ($a->sequencingQualityControl->q30 + $b->sequencingQualityControl->q30) / 2,
+            ($a->sequencingQualityControl->phasing + $b->sequencingQualityControl->phasing) / 2,
+            ($a->sequencingQualityControl->prephasing + $b->sequencingQualityControl->prephasing) / 2,
+            $aligned,
+            $error
+        );
+
+        return new self(
+            $clusterStatistic,
+            $sequencingQualityControl,
+            (int) (($a->intensityCycle + $b->intensityCycle) / 2),
+            $a->yield + $b->yield
+        );
+    }
+}
diff --git a/tests/GenomicRegionTest.php b/tests/GenomicRegionTest.php
index 7ad4e73..244b63a 100644
--- a/tests/GenomicRegionTest.php
+++ b/tests/GenomicRegionTest.php
@@ -268,7 +268,7 @@ public function testGenomicPositions(): void
         $positions = $region->genomicPositions();
 
         self::assertCount(4, $positions);
-        self::assertEquals($region->length(), count($positions));
+        self::assertCount($region->length(), $positions);
 
         self::assertTrue($positions[0]->equals(GenomicPosition::parseOneBased('chr11:10')));
         self::assertTrue($positions[1]->equals(GenomicPosition::parseOneBased('chr11:11')));
diff --git a/tests/InterOp/DeviationValueTest.php b/tests/InterOp/DeviationValueTest.php
new file mode 100644
index 0000000..e1eaf79
--- /dev/null
+++ b/tests/InterOp/DeviationValueTest.php
@@ -0,0 +1,36 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\InterOp;
+
+use MLL\Utils\InterOp\DeviationValue;
+use PHPUnit\Framework\Attributes\DataProvider;
+use PHPUnit\Framework\TestCase;
+
+final class DeviationValueTest extends TestCase
+{
+    /** @dataProvider parseProvider */
+    #[DataProvider('parseProvider')]
+    public function testParse(string $input, ?float $expectedValue, ?float $expectedDeviation): void
+    {
+        $result = DeviationValue::parse($input);
+
+        if ($expectedValue === null) {
+            self::assertNull($result);
+
+            return;
+        }
+
+        self::assertNotNull($result);
+        self::assertSame($expectedValue, $result->value);
+        self::assertSame($expectedDeviation, $result->deviation);
+    }
+
+    /** @return iterable<string, array{string, float|null, float|null}> */
+    public static function parseProvider(): iterable
+    {
+        yield 'integer values' => ['851 +/- 32', 851.0, 32.0];
+        yield 'decimal values' => ['96.54 +/- 0.25', 96.54, 0.25];
+        yield 'nan returns null' => ['nan +/- nan', null, null];
+        yield 'small decimal values' => ['0.085 +/- 0.020', 0.085, 0.02];
+    }
+}
diff --git a/tests/InterOp/InterOpResultTest.php b/tests/InterOp/InterOpResultTest.php
new file mode 100644
index 0000000..09b6559
--- /dev/null
+++ b/tests/InterOp/InterOpResultTest.php
@@ -0,0 +1,69 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\InterOp;
+
+use MLL\Utils\InterOp\InterOpResult;
+use PHPUnit\Framework\Attributes\DataProvider;
+use PHPUnit\Framework\TestCase;
+
+final class InterOpResultTest extends TestCase
+{
+    /**
+     * @dataProvider dataReadDetectionProvider
+     *
+     * @param array<int, array<string, string>> $summary
+     */
+    #[DataProvider('dataReadDetectionProvider')]
+    public function testFindDataReads(string $description, array $summary, string $expectedFirst, string $expectedLast): void
+    {
+        [$first, $last] = InterOpResult::findDataReads($summary);
+
+        self::assertSame($expectedFirst, $first, "{$description}: first data read");
+        self::assertSame($expectedLast, $last, "{$description}: last data read");
+    }
+
+    /** @return iterable<string, array{string, array<int, array<string, string>>, string, string}> */
+    public static function dataReadDetectionProvider(): iterable
+    {
+        yield 'MiSeq single-index' => [
+            'MiSeq with one index read',
+            [
+                ['Level' => 'Read 1'],
+                ['Level' => 'Read 2 (I)'],
+                ['Level' => 'Read 3'],
+                ['Level' => 'Non-indexed'],
+                ['Level' => 'Total'],
+            ],
+            'Read 1',
+            'Read 3',
+        ];
+
+        yield 'MiSeq dual-index' => [
+            'MiSeq with two index reads',
+            [
+                ['Level' => 'Read 1'],
+                ['Level' => 'Read 2 (I)'],
+                ['Level' => 'Read 3 (I)'],
+                ['Level' => 'Read 4'],
+                ['Level' => 'Non-indexed'],
+                ['Level' => 'Total'],
+            ],
+            'Read 1',
+            'Read 4',
+        ];
+
+        yield 'i100 dual-index' => [
+            'i100 with index reads first',
+            [
+                ['Level' => 'Read 1 (I)'],
+                ['Level' => 'Read 2 (I)'],
+                ['Level' => 'Read 3'],
+                ['Level' => 'Read 4'],
+                ['Level' => 'Non-indexed'],
+                ['Level' => 'Total'],
+            ],
+            'Read 3',
+            'Read 4',
+        ];
+    }
+}
diff --git a/tests/InterOp/meta-info-i100.json b/tests/InterOp/meta-info-i100.json
new file mode 100644
index 0000000..a7fc762
--- /dev/null
+++ b/tests/InterOp/meta-info-i100.json
@@ -0,0 +1,256 @@
+{
+  "runParameters": {
+    "xml": {
+      "@version": 1,
+      "@encoding": "utf-8"
+    },
+    "RunParameters": {
+      "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
+      "@xmlns:xsd": "http://www.w3.org/2001/XMLSchema",
+      "Application": "MiSeqi100Series Control Software",
+      "SystemSuiteVersion": "1.1.0.26158",
+      "OutputFolder": "//192.168.0.228/miseq_active/miSeqi100/20260205_SH01038_0007_ASC2139476-SC3",
+      "CustomPrimerSelections": {
+        "ReadOnePrimer": false,
+        "ReadTwoPrimer": false,
+        "IndexOnePrimer": false,
+        "IndexTwoPrimer": false
+      },
+      "CloudUploadMode": "InstrumentPerformance",
+      "RunSetupMode": "Manual",
+      "SecondaryAnalysisMode": "ManualModeLocalAnalysis",
+      "InstrumentType": "MiSeqi100Plus",
+      "InstrumentSerialNumber": "SH01038",
+      "RunId": "20260205_SH01038_0007_ASC2139476-SC3",
+      "SampleSheetName": "SampleSheet.csv",
+      "ConsumableInfo": {
+        "ConsumableInfo": [
+          {
+            "SerialNumber": "SC2139476-SC3",
+            "LotNumber": 20987817,
+            "PartNumber": 20115216,
+            "ExpirationDate": "2026-07-29T00:00:00+02:00",
+            "Type": "DryCartridge",
+            "Mode": "5M",
+            "Version": 1
+          },
+          {
+            "SerialNumber": "SC2157208-SC2",
+            "LotNumber": 20994302,
+            "PartNumber": 20079747,
+            "ExpirationDate": "2026-10-17T00:00:00+02:00",
+            "Type": "WetCartridge",
+            "Mode": "B",
+            "Version": 1
+          },
+          {
+            "SerialNumber": "BXA23202-0617",
+            "Type": "FlowCell_1",
+            "Mode": 1,
+            "Version": 1
+          }
+        ]
+      },
+      "PlannedReads": {
+        "Read": [
+          {
+            "@ReadName": "Index1",
+            "@Cycles": 6,
+            "#text": null
+          },
+          {
+            "@ReadName": "Index2",
+            "@Cycles": 8,
+            "#text": null
+          },
+          {
+            "@ReadName": "Read1",
+            "@Cycles": 301,
+            "#text": null
+          },
+          {
+            "@ReadName": "Read2",
+            "@Cycles": 301,
+            "#text": null
+          }
+        ]
+      },
+      "SecondaryAnalysisInfo": {
+        "SecondaryAnalysisInfo": {
+          "SecondaryAnalysisPlatformVersion": "4.4.6",
+          "SecondaryAnalysisWorkflow": {
+            "string": "DRAGEN BCL Convert"
+          }
+        }
+      },
+      "RunCounter": 7,
+      "RecipeName": "5M/600_B_Recipe",
+      "RecipeVersion": "2.2_IF",
+      "ExperimentName": "Run9619",
+      "PurgeReagentCartridge": true
+    }
+  },
+  "interop": {
+    "summary": [
+      {
+        "Level": "Read 1 (I)",
+        "Yield": "0.02",
+        "Projected Yield": "0.02",
+        "Aligned": "0.00",
+        "Error Rate": "nan",
+        "Intensity C1": "3031",
+        "%>=Q30": "92.66",
+        "% Occupied": "74.22"
+      },
+      {
+        "Level": "Read 2 (I)",
+        "Yield": "0.03",
+        "Projected Yield": "0.03",
+        "Aligned": "0.00",
+        "Error Rate": "nan",
+        "Intensity C1": "2979",
+        "%>=Q30": "92.00",
+        "% Occupied": "74.22"
+      },
+      {
+        "Level": "Read 3",
+        "Yield": "1.49",
+        "Projected Yield": "1.49",
+        "Aligned": "28.66",
+        "Error Rate": "0.27",
+        "Intensity C1": "3534",
+        "%>=Q30": "95.35",
+        "% Occupied": "74.22"
+      },
+      {
+        "Level": "Read 4",
+        "Yield": "1.49",
+        "Projected Yield": "1.49",
+        "Aligned": "28.27",
+        "Error Rate": "0.32",
+        "Intensity C1": "3486",
+        "%>=Q30": "96.32",
+        "% Occupied": "74.22"
+      },
+      {
+        "Level": "Non-indexed",
+        "Yield": "2.97",
+        "Projected Yield": "2.97",
+        "Aligned": "28.47",
+        "Error Rate": "0.29",
+        "Intensity C1": "3510",
+        "%>=Q30": "95.83",
+        "% Occupied": "74.22"
+      },
+      {
+        "Level": "Total",
+        "Yield": "3.03",
+        "Projected Yield": "3.03",
+        "Aligned": "28.47",
+        "Error Rate": "0.29",
+        "Intensity C1": "3257",
+        "%>=Q30": "95.76",
+        "% Occupied": "74.22"
+      }
+    ],
+    "reads": {
+      "Read 1 (I)": [
+        {
+          "Lane": "1",
+          "Surface": "-",
+          "Tiles": "18",
+          "Density": "1000 +/- 0",
+          "Cluster PF": "62.27 +/- 0.43",
+          "Legacy Phasing/Prephasing Rate": "nan / nan",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "7.91",
+          "Reads PF": "4.92",
+          "%>=Q30": "92.66",
+          "Yield": "0.02",
+          "Cycles Error": "0",
+          "Aligned": "nan +/- nan",
+          "Error": "nan +/- nan",
+          "Error (35)": "nan +/- nan",
+          "Error (75)": "nan +/- nan",
+          "Error (100)": "nan +/- nan",
+          "% Occupied": "74.22 +/- 0.34",
+          "Intensity C1": "3031 +/- 83"
+        }
+      ],
+      "Read 2 (I)": [
+        {
+          "Lane": "1",
+          "Surface": "-",
+          "Tiles": "18",
+          "Density": "1000 +/- 0",
+          "Cluster PF": "62.27 +/- 0.43",
+          "Legacy Phasing/Prephasing Rate": "nan / nan",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "7.91",
+          "Reads PF": "4.92",
+          "%>=Q30": "92.00",
+          "Yield": "0.03",
+          "Cycles Error": "0",
+          "Aligned": "nan +/- nan",
+          "Error": "nan +/- nan",
+          "Error (35)": "nan +/- nan",
+          "Error (75)": "nan +/- nan",
+          "Error (100)": "nan +/- nan",
+          "% Occupied": "74.22 +/- 0.34",
+          "Intensity C1": "2978 +/- 61"
+        }
+      ],
+      "Read 3": [
+        {
+          "Lane": "1",
+          "Surface": "-",
+          "Tiles": "18",
+          "Density": "1000 +/- 0",
+          "Cluster PF": "62.27 +/- 0.43",
+          "Legacy Phasing/Prephasing Rate": "0.075 / 0.042",
+          "Phasing  slope/offset": "0.060 / -0.469",
+          "Prephasing slope/offset": "0.023 / 0.863",
+          "Reads": "7.91",
+          "Reads PF": "4.92",
+          "%>=Q30": "95.35",
+          "Yield": "1.49",
+          "Cycles Error": "300",
+          "Aligned": "28.66 +/- 0.56",
+          "Error": "0.27 +/- 0.01",
+          "Error (35)": "0.09 +/- 0.01",
+          "Error (75)": "0.08 +/- 0.00",
+          "Error (100)": "0.11 +/- 0.00",
+          "% Occupied": "74.22 +/- 0.34",
+          "Intensity C1": "3534 +/- 79"
+        }
+      ],
+      "Read 4": [
+        {
+          "Lane": "1",
+          "Surface": "-",
+          "Tiles": "18",
+          "Density": "1000 +/- 0",
+          "Cluster PF": "62.27 +/- 0.43",
+          "Legacy Phasing/Prephasing Rate": "0.025 / 0.001",
+          "Phasing  slope/offset": "0.065 / -0.990",
+          "Prephasing slope/offset": "0.029 / 0.350",
+          "Reads": "7.91",
+          "Reads PF": "4.92",
+          "%>=Q30": "96.32",
+          "Yield": "1.49",
+          "Cycles Error": "300",
+          "Aligned": "28.27 +/- 0.56",
+          "Error": "0.32 +/- 0.01",
+          "Error (35)": "0.09 +/- 0.00",
+          "Error (75)": "0.21 +/- 0.01",
+          "Error (100)": "0.26 +/- 0.01",
+          "% Occupied": "74.22 +/- 0.34",
+          "Intensity C1": "3486 +/- 89"
+        }
+      ]
+    }
+  },
+  "uncPath": "mllsrv20/miseq_active\\miSeqi100\\20260205_SH01038_0007_ASC2139476-SC3\\meta-info.json"
+}
\ No newline at end of file
diff --git a/tests/InterOp/meta-info-miseq.json b/tests/InterOp/meta-info-miseq.json
new file mode 100644
index 0000000..d69b8e0
--- /dev/null
+++ b/tests/InterOp/meta-info-miseq.json
@@ -0,0 +1,360 @@
+{
+  "runParameters": {
+    "xml": {
+      "@version": 1
+    },
+    "RunParameters": {
+      "@xmlns:xsd": "http://www.w3.org/2001/XMLSchema",
+      "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
+      "EnableCloud": false,
+      "RunParametersVersion": "MiSeq_1_1",
+      "CopyManifests": true,
+      "FlowcellRFIDTag": {
+        "SerialNumber": "000000000-KT6CY",
+        "PartNumber": 15028382,
+        "ExpirationDate": "2023-09-27T00:00:00"
+      },
+      "PR2BottleRFIDTag": {
+        "SerialNumber": "MS3471919-00PR2",
+        "PartNumber": 15041807,
+        "ExpirationDate": "2023-09-28T00:00:00"
+      },
+      "ReagentKitRFIDTag": {
+        "SerialNumber": "MS3233206-600V3",
+        "PartNumber": 15043962,
+        "ExpirationDate": "2023-09-16T00:00:00"
+      },
+      "Resumable": true,
+      "ManifestFiles": null,
+      "AfterRunWashMethod": "Post-Run Wash",
+      "Setup": {
+        "SupportMultipleSurfacesInUI": true,
+        "ApplicationVersion": "2.6.2.2",
+        "NumTilesPerSwath": 19,
+        "NumSwaths": 1,
+        "NumLanes": 1,
+        "ApplicationName": "MiSeq Control Software"
+      },
+      "RunID": "230421_M02074_0859_000000000-KT6CY",
+      "ScannerID": "M02074",
+      "RunNumber": 859,
+      "FPGAVersion": "9.5.12",
+      "MCSVersion": "2.6.2.2",
+      "RTAVersion": "1.18.54",
+      "Barcode": "000000000-KT6CY",
+      "PR2BottleBarcode": "MS3471919-00PR2",
+      "ReagentKitPartNumberEntered": 15043962,
+      "ReagentKitVersion": "Version3",
+      "ReagentKitBarcode": "MS3233206-600V3",
+      "PreviousPR2BottleBarcode": null,
+      "PreviousReagentKitBarcode": null,
+      "Chemistry": "Default",
+      "Username": "sbsuser",
+      "Workflow": {
+        "Analysis": "GenerateFASTQ"
+      },
+      "EnableAnalysis": false,
+      "Reads": {
+        "RunInfoRead": [
+          {
+            "@Number": 1,
+            "@NumCycles": 301,
+            "@IsIndexedRead": "N",
+            "#text": null
+          },
+          {
+            "@Number": 2,
+            "@NumCycles": 6,
+            "@IsIndexedRead": "Y",
+            "#text": null
+          },
+          {
+            "@Number": 3,
+            "@NumCycles": 301,
+            "@IsIndexedRead": "N",
+            "#text": null
+          }
+        ]
+      },
+      "TempFolder": "D:\\Illumina\\MiSeqTemp\\230421_M02074_0859_000000000-KT6CY",
+      "AnalysisFolder": "D:\\Illumina\\MiSeqAnalysis\\230421_M02074_0859_000000000-KT6CY",
+      "RunStartDate": 230421,
+      "MostRecentWashType": "PostRun",
+      "RecipeFolder": "D:\\Illumina\\MiSeq Control Software\\CustomRecipe",
+      "ILMNOnlyRecipeFolder": "C:\\Illumina\\MiSeq Control Software\\Recipe",
+      "SampleSheetName": "Run7054-IMMUNORECEPTOR",
+      "SampleSheetFolder": "Z:\\samplesheets",
+      "ManifestFolder": "Z:\\manifests",
+      "OutputFolder": "Z:\\230421_M02074_0859_000000000-KT6CY",
+      "FocusMethod": "AutoFocus",
+      "SurfaceToScan": "Both",
+      "SaveFocusImages": false,
+      "SaveScanImages": true,
+      "CloudUsername": null,
+      "RunManagementType": "Standalone",
+      "CloudRunId": 257422183,
+      "SendInstrumentHealthToILMN": true
+    }
+  },
+  "interop": {
+    "summary": [
+      {
+        "Level": "Read 1",
+        "Yield": "6.14",
+        "Projected Yield": "6.14",
+        "Aligned": "6.18",
+        "Error Rate": "2.88",
+        "Intensity C1": "139",
+        "%>=Q30": "88.20",
+        "% Occupied": "nan"
+      },
+      {
+        "Level": "Read 2 (I)",
+        "Yield": "0.10",
+        "Projected Yield": "0.10",
+        "Aligned": "0.00",
+        "Error Rate": "nan",
+        "Intensity C1": "343",
+        "%>=Q30": "91.89",
+        "% Occupied": "nan"
+      },
+      {
+        "Level": "Read 3",
+        "Yield": "6.14",
+        "Projected Yield": "6.14",
+        "Aligned": "6.04",
+        "Error Rate": "3.18",
+        "Intensity C1": "46",
+        "%>=Q30": "78.19",
+        "% Occupied": "nan"
+      },
+      {
+        "Level": "Non-indexed",
+        "Yield": "12.29",
+        "Projected Yield": "12.29",
+        "Aligned": "6.11",
+        "Error Rate": "3.03",
+        "Intensity C1": "92",
+        "%>=Q30": "83.20",
+        "% Occupied": "nan"
+      },
+      {
+        "Level": "Total",
+        "Yield": "12.39",
+        "Projected Yield": "12.39",
+        "Aligned": "6.11",
+        "Error Rate": "3.03",
+        "Intensity C1": "176",
+        "%>=Q30": "83.27",
+        "% Occupied": "nan"
+      }
+    ],
+    "reads": {
+      "Read 1": [
+        {
+          "Lane": "1",
+          "Surface": "-",
+          "Tiles": "38",
+          "Density": "851 +/- 32",
+          "Cluster PF": "96.54 +/- 0.25",
+          "Legacy Phasing/Prephasing Rate": "0.085 / 0.020",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "21.22",
+          "Reads PF": "20.48",
+          "%>=Q30": "88.20",
+          "Yield": "6.14",
+          "Cycles Error": "300",
+          "Aligned": "6.18 +/- 0.05",
+          "Error": "2.88 +/- 0.07",
+          "Error (35)": "0.15 +/- 0.03",
+          "Error (75)": "0.19 +/- 0.02",
+          "Error (100)": "0.27 +/- 0.03",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "139 +/- 12"
+        },
+        {
+          "Lane": "1",
+          "Surface": "1",
+          "Tiles": "19",
+          "Density": "869 +/- 29",
+          "Cluster PF": "96.54 +/- 0.30",
+          "Legacy Phasing/Prephasing Rate": "0.085 / 0.015",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "10.81",
+          "Reads PF": "10.44",
+          "%>=Q30": "88.34",
+          "Yield": "3.13",
+          "Cycles Error": "-",
+          "Aligned": "6.18 +/- 0.05",
+          "Error": "2.92 +/- 0.06",
+          "Error (35)": "0.15 +/- 0.03",
+          "Error (75)": "0.20 +/- 0.02",
+          "Error (100)": "0.29 +/- 0.03",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "151 +/- 3"
+        },
+        {
+          "Lane": "1",
+          "Surface": "2",
+          "Tiles": "19",
+          "Density": "834 +/- 25",
+          "Cluster PF": "96.53 +/- 0.19",
+          "Legacy Phasing/Prephasing Rate": "0.085 / 0.025",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "10.40",
+          "Reads PF": "10.04",
+          "%>=Q30": "88.05",
+          "Yield": "3.01",
+          "Cycles Error": "-",
+          "Aligned": "6.17 +/- 0.05",
+          "Error": "2.83 +/- 0.04",
+          "Error (35)": "0.15 +/- 0.02",
+          "Error (75)": "0.19 +/- 0.02",
+          "Error (100)": "0.26 +/- 0.02",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "128 +/- 3"
+        }
+      ],
+      "Read 2 (I)": [
+        {
+          "Lane": "1",
+          "Surface": "-",
+          "Tiles": "38",
+          "Density": "851 +/- 32",
+          "Cluster PF": "96.54 +/- 0.25",
+          "Legacy Phasing/Prephasing Rate": "0.000 / 0.000",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "21.22",
+          "Reads PF": "20.48",
+          "%>=Q30": "91.89",
+          "Yield": "0.10",
+          "Cycles Error": "0",
+          "Aligned": "nan +/- nan",
+          "Error": "nan +/- nan",
+          "Error (35)": "nan +/- nan",
+          "Error (75)": "nan +/- nan",
+          "Error (100)": "nan +/- nan",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "343 +/- 26"
+        },
+        {
+          "Lane": "1",
+          "Surface": "1",
+          "Tiles": "19",
+          "Density": "869 +/- 29",
+          "Cluster PF": "96.54 +/- 0.30",
+          "Legacy Phasing/Prephasing Rate": "nan / nan",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "10.81",
+          "Reads PF": "10.44",
+          "%>=Q30": "91.99",
+          "Yield": "0.05",
+          "Cycles Error": "-",
+          "Aligned": "nan +/- nan",
+          "Error": "nan +/- nan",
+          "Error (35)": "nan +/- nan",
+          "Error (75)": "nan +/- nan",
+          "Error (100)": "nan +/- nan",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "368 +/- 6"
+        },
+        {
+          "Lane": "1",
+          "Surface": "2",
+          "Tiles": "19",
+          "Density": "834 +/- 25",
+          "Cluster PF": "96.53 +/- 0.19",
+          "Legacy Phasing/Prephasing Rate": "nan / nan",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "10.40",
+          "Reads PF": "10.04",
+          "%>=Q30": "91.79",
+          "Yield": "0.05",
+          "Cycles Error": "-",
+          "Aligned": "nan +/- nan",
+          "Error": "nan +/- nan",
+          "Error (35)": "nan +/- nan",
+          "Error (75)": "nan +/- nan",
+          "Error (100)": "nan +/- nan",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "318 +/- 5"
+        }
+      ],
+      "Read 3": [
+        {
+          "Lane": "1",
+          "Surface": "-",
+          "Tiles": "38",
+          "Density": "851 +/- 32",
+          "Cluster PF": "96.54 +/- 0.25",
+          "Legacy Phasing/Prephasing Rate": "0.045 / 0.016",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "21.22",
+          "Reads PF": "20.48",
+          "%>=Q30": "78.19",
+          "Yield": "6.14",
+          "Cycles Error": "300",
+          "Aligned": "6.04 +/- 0.06",
+          "Error": "3.18 +/- 0.06",
+          "Error (35)": "0.25 +/- 0.02",
+          "Error (75)": "0.30 +/- 0.02",
+          "Error (100)": "0.38 +/- 0.02",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "46 +/- 4"
+        },
+        {
+          "Lane": "1",
+          "Surface": "1",
+          "Tiles": "19",
+          "Density": "869 +/- 29",
+          "Cluster PF": "96.54 +/- 0.30",
+          "Legacy Phasing/Prephasing Rate": "0.058 / 0.028",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "10.81",
+          "Reads PF": "10.44",
+          "%>=Q30": "78.61",
+          "Yield": "3.13",
+          "Cycles Error": "-",
+          "Aligned": "6.05 +/- 0.05",
+          "Error": "3.16 +/- 0.06",
+          "Error (35)": "0.24 +/- 0.02",
+          "Error (75)": "0.31 +/- 0.01",
+          "Error (100)": "0.38 +/- 0.02",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "50 +/- 2"
+        },
+        {
+          "Lane": "1",
+          "Surface": "2",
+          "Tiles": "19",
+          "Density": "834 +/- 25",
+          "Cluster PF": "96.53 +/- 0.19",
+          "Legacy Phasing/Prephasing Rate": "0.031 / 0.003",
+          "Phasing  slope/offset": "nan / nan",
+          "Prephasing slope/offset": "nan / nan",
+          "Reads": "10.40",
+          "Reads PF": "10.04",
+          "%>=Q30": "77.76",
+          "Yield": "3.01",
+          "Cycles Error": "-",
+          "Aligned": "6.02 +/- 0.05",
+          "Error": "3.20 +/- 0.06",
+          "Error (35)": "0.25 +/- 0.03",
+          "Error (75)": "0.30 +/- 0.02",
+          "Error (100)": "0.37 +/- 0.02",
+          "% Occupied": "nan +/- nan",
+          "Intensity C1": "41 +/- 1"
+        }
+      ]
+    }
+  },
+  "uncPath": "mllsrv20/miseq_active\\230421_M02074_0859_000000000-KT6CY\\meta-info.json"
+}
\ No newline at end of file

From e27b9e7b62d15944778e8941b685917628fdf4d7 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 10:58:09 +0200
Subject: [PATCH 02/25] feat: implement interop

---
 src/InterOp/MetaInfo.php                 |  31 +++++
 src/InterOp/RunParameters.php            | 148 +++++++++++++++++++++++
 src/InterOp/RunResult.php                |  25 ++++
 src/InterOp/SequencingQualityControl.php |  30 +++++
 tests/InterOp/MetaInfoTest.php           |  93 ++++++++++++++
 5 files changed, 327 insertions(+)
 create mode 100644 src/InterOp/MetaInfo.php
 create mode 100644 src/InterOp/RunParameters.php
 create mode 100644 src/InterOp/RunResult.php
 create mode 100644 src/InterOp/SequencingQualityControl.php
 create mode 100644 tests/InterOp/MetaInfoTest.php

diff --git a/src/InterOp/MetaInfo.php b/src/InterOp/MetaInfo.php
new file mode 100644
index 0000000..ef5ec8a
--- /dev/null
+++ b/src/InterOp/MetaInfo.php
@@ -0,0 +1,31 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+use function Safe\json_decode;
+
+/**
+ * @phpstan-import-type MiSeqParams from RunParameters
+ * @phpstan-import-type I100Params from RunParameters
+ */
+class MetaInfo
+{
+    /** @var RunParameters */
+    public $runParameters;
+
+    /** @var InterOpResult */
+    public $interOpResult;
+
+    /** @var string */
+    public $uncPath;
+
+    public function __construct(string $json)
+    {
+        /** @var array{runParameters: array{RunParameters: MiSeqParams|I100Params}, interop: array{summary: array<int, array<string, string>>, reads: array<string, array<int, array<string, string>>>}, uncPath: string} $data */
+        $data = json_decode($json, true);
+
+        $this->runParameters = new RunParameters($data['runParameters']['RunParameters']);
+        $this->interOpResult = new InterOpResult($data['interop']['summary'], $data['interop']['reads']);
+        $this->uncPath = $data['uncPath'];
+    }
+}
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
new file mode 100644
index 0000000..0eaf4d1
--- /dev/null
+++ b/src/InterOp/RunParameters.php
@@ -0,0 +1,148 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+use Carbon\Carbon;
+
+/**
+ * @phpstan-type RFIDTag array{SerialNumber: string, PartNumber: int, ExpirationDate: string}
+ * @phpstan-type MiSeqParams array{Setup: array{ApplicationName: string}, RunID: string, MCSVersion: string, RTAVersion: string, RunStartDate: int, FlowcellRFIDTag: RFIDTag, PR2BottleRFIDTag?: RFIDTag, ReagentKitRFIDTag?: RFIDTag}
+ * @phpstan-type Consumable array{SerialNumber: string, Type: string, ExpirationDate?: string, LotNumber?: int, PartNumber?: int, Mode?: string|int, Version?: int}
+ * @phpstan-type I100Params array{Application: string, RunId: string, SystemSuiteVersion: string, ConsumableInfo: array{ConsumableInfo: array<int, Consumable>}}
+ */
+class RunParameters
+{
+    public const APPLICATION_MISEQ = 'MiSeq Control Software';
+    public const APPLICATION_MISEQ_I100 = 'MiSeqi100Series Control Software';
+
+    /** @var string */
+    public $application;
+
+    /** @var Carbon */
+    public $runDate;
+
+    /** @var string */
+    public $flowcell;
+
+    /** @var string */
+    public $flowcellExpirationDate;
+
+    /** @var string */
+    public $rta;
+
+    /** @var string RunID / RunId. */
+    public $info;
+
+    /** @var string MCS / system suite version. */
+    public $mcs;
+
+    /** @var array<int, array{name: string, expire_date: string}> */
+    public $reagents;
+
+    /** @param MiSeqParams|I100Params $params */
+    public function __construct(array $params)
+    {
+        if (isset($params['Setup']['ApplicationName'])) {
+            $this->parseMiSeq($params);
+        } elseif (isset($params['Application'])) {
+            $this->parseMiSeqI100($params);
+        } else {
+            throw new InterOpException('Unable to determine device type from RunParameters.');
+        }
+    }
+
+    /** @param MiSeqParams $params */
+    private function parseMiSeq(array $params): void
+    {
+        $this->application = $params['Setup']['ApplicationName'];
+        $this->info = $params['RunID'];
+        $this->mcs = $params['MCSVersion'];
+        $this->rta = $params['RTAVersion'];
+
+        $runStartDate = (string) $params['RunStartDate'];
+        $date = Carbon::createFromFormat('!ymd', $runStartDate);
+        assert($date instanceof Carbon, "Failed to parse MiSeq RunStartDate: {$runStartDate}");
+        $this->runDate = $date;
+
+        $this->flowcell = $this->stripZeroPrefix($params['FlowcellRFIDTag']['SerialNumber']);
+        $this->flowcellExpirationDate = $this->formatExpirationDate($params['FlowcellRFIDTag']['ExpirationDate']);
+
+        $this->reagents = [];
+
+        if (isset($params['PR2BottleRFIDTag'])) {
+            $this->reagents[] = [
+                'name' => $params['PR2BottleRFIDTag']['SerialNumber'],
+                'expire_date' => $this->formatExpirationDate($params['PR2BottleRFIDTag']['ExpirationDate']),
+            ];
+        }
+
+        if (isset($params['ReagentKitRFIDTag'])) {
+            $this->reagents[] = [
+                'name' => $params['ReagentKitRFIDTag']['SerialNumber'],
+                'expire_date' => $this->formatExpirationDate($params['ReagentKitRFIDTag']['ExpirationDate']),
+            ];
+        }
+    }
+
+    /** @param I100Params $params */
+    private function parseMiSeqI100(array $params): void
+    {
+        $this->application = $params['Application'];
+        $this->info = $params['RunId'];
+        $this->mcs = $params['SystemSuiteVersion'];
+        $this->rta = '';
+
+        $runID = $params['RunId'];
+        $dateString = substr($runID, 0, 8);
+        $date = Carbon::createFromFormat('!Ymd', $dateString);
+        assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$runID}");
+        $this->runDate = $date;
+
+        $consumables = $params['ConsumableInfo']['ConsumableInfo'];
+        $this->flowcell = '';
+        $this->flowcellExpirationDate = '';
+        $this->reagents = [];
+
+        foreach ($consumables as $consumable) {
+            $type = $consumable['Type'];
+
+            if ($type === 'DryCartridge') {
+                $this->flowcell = $consumable['SerialNumber'];
+                if (isset($consumable['ExpirationDate'])) {
+                    $this->flowcellExpirationDate = $this->formatExpirationDate($consumable['ExpirationDate']);
+                }
+            }
+
+            if ($type === 'DryCartridge' || $type === 'WetCartridge') {
+                $this->reagents[] = [
+                    'name' => $consumable['SerialNumber'],
+                    'expire_date' => isset($consumable['ExpirationDate'])
+                        ? $this->formatExpirationDate($consumable['ExpirationDate'])
+                        : '',
+                ];
+            }
+        }
+    }
+
+    private function stripZeroPrefix(string $serial): string
+    {
+        $pos = strpos($serial, '-');
+        if ($pos === false) {
+            return $serial;
+        }
+
+        $prefix = substr($serial, 0, $pos);
+        if ($prefix !== '' && trim($prefix, '0') === '') {
+            return substr($serial, $pos + 1);
+        }
+
+        return $serial;
+    }
+
+    private function formatExpirationDate(string $dateTime): string
+    {
+        $date = Carbon::parse($dateTime);
+
+        return $date->format('Y-m-d');
+    }
+}
diff --git a/src/InterOp/RunResult.php b/src/InterOp/RunResult.php
new file mode 100644
index 0000000..a496dff
--- /dev/null
+++ b/src/InterOp/RunResult.php
@@ -0,0 +1,25 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+class RunResult
+{
+    /** @var ClusterStatistic */
+    public $clusterStatistic;
+
+    /** @var SequencingQualityControl */
+    public $sequencingQualityControl;
+
+    public function __construct(ClusterStatistic $clusterStatistic, SequencingQualityControl $sequencingQualityControl)
+    {
+        $this->clusterStatistic = $clusterStatistic;
+        $this->sequencingQualityControl = $sequencingQualityControl;
+    }
+
+    public static function fromLaneResults(LaneResult $read1, LaneResult $read2): self
+    {
+        $aggregated = LaneResult::aggregate($read1, $read2);
+
+        return new self($aggregated->clusterStatistic, $aggregated->sequencingQualityControl);
+    }
+}
diff --git a/src/InterOp/SequencingQualityControl.php b/src/InterOp/SequencingQualityControl.php
new file mode 100644
index 0000000..52b8389
--- /dev/null
+++ b/src/InterOp/SequencingQualityControl.php
@@ -0,0 +1,30 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\InterOp;
+
+class SequencingQualityControl
+{
+    /** @var float Percentage of bases with quality score >= Q30. */
+    public $q30;
+
+    /** @var float Phasing rate. */
+    public $phasing;
+
+    /** @var float Prephasing rate. */
+    public $prephasing;
+
+    /** @var DeviationValue Alignment percentage. */
+    public $aligned;
+
+    /** @var DeviationValue Error rate. */
+    public $error;
+
+    public function __construct(float $q30, float $phasing, float $prephasing, DeviationValue $aligned, DeviationValue $error)
+    {
+        $this->q30 = $q30;
+        $this->phasing = $phasing;
+        $this->prephasing = $prephasing;
+        $this->aligned = $aligned;
+        $this->error = $error;
+    }
+}
diff --git a/tests/InterOp/MetaInfoTest.php b/tests/InterOp/MetaInfoTest.php
new file mode 100644
index 0000000..145de60
--- /dev/null
+++ b/tests/InterOp/MetaInfoTest.php
@@ -0,0 +1,93 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\InterOp;
+
+use MLL\Utils\InterOp\MetaInfo;
+use MLL\Utils\InterOp\RunParameters;
+use PHPUnit\Framework\TestCase;
+
+use function Safe\file_get_contents;
+
+final class MetaInfoTest extends TestCase
+{
+    public function testParseMiSeq(): void
+    {
+        $json = file_get_contents(__DIR__ . '/meta-info-miseq.json');
+        $metaInfo = new MetaInfo($json);
+
+        self::assertSame(RunParameters::APPLICATION_MISEQ, $metaInfo->runParameters->application);
+        self::assertSame('2023-04-21', $metaInfo->runParameters->runDate->format('Y-m-d'));
+        self::assertSame('KT6CY', $metaInfo->runParameters->flowcell);
+        self::assertSame('2023-09-27', $metaInfo->runParameters->flowcellExpirationDate);
+        self::assertSame('1.18.54', $metaInfo->runParameters->rta);
+        self::assertSame('2.6.2.2', $metaInfo->runParameters->mcs);
+        self::assertSame('230421_M02074_0859_000000000-KT6CY', $metaInfo->runParameters->info);
+
+        self::assertCount(2, $metaInfo->runParameters->reagents);
+        self::assertSame('MS3471919-00PR2', $metaInfo->runParameters->reagents[0]['name']);
+        self::assertSame('2023-09-28', $metaInfo->runParameters->reagents[0]['expire_date']);
+        self::assertSame('MS3233206-600V3', $metaInfo->runParameters->reagents[1]['name']);
+        self::assertSame('2023-09-16', $metaInfo->runParameters->reagents[1]['expire_date']);
+
+        self::assertSame(851.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->value);
+        self::assertSame(32.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->deviation);
+        self::assertSame(96.54, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterPF->value);
+        self::assertSame(21.22, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCount);
+        self::assertSame(20.48, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCountPF);
+
+        self::assertSame(88.2, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->q30);
+        self::assertSame(0.085, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->phasing);
+        self::assertSame(0.02, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->prephasing);
+        self::assertSame(6.18, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->aligned->value);
+        self::assertSame(2.88, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->error->value);
+        self::assertSame(139, $metaInfo->interOpResult->resultsForRead1->intensityCycle);
+        self::assertSame(6140000, $metaInfo->interOpResult->resultsForRead1->yield);
+
+        self::assertSame(78.19, $metaInfo->interOpResult->resultsForRead2->sequencingQualityControl->q30);
+        self::assertSame(0.045, $metaInfo->interOpResult->resultsForRead2->sequencingQualityControl->phasing);
+        self::assertSame(46, $metaInfo->interOpResult->resultsForRead2->intensityCycle);
+        self::assertSame(6140000, $metaInfo->interOpResult->resultsForRead2->yield);
+
+        $runQC = $metaInfo->interOpResult->resultsForRun->sequencingQualityControl;
+        self::assertEqualsWithDelta(83.195, $runQC->q30, 0.001);
+        self::assertEqualsWithDelta(0.065, $runQC->phasing, 0.001);
+
+        self::assertSame('mllsrv20/miseq_active\\230421_M02074_0859_000000000-KT6CY\\meta-info.json', $metaInfo->uncPath);
+    }
+
+    public function testParseMiSeqI100(): void
+    {
+        $json = file_get_contents(__DIR__ . '/meta-info-i100.json');
+        $metaInfo = new MetaInfo($json);
+
+        self::assertSame(RunParameters::APPLICATION_MISEQ_I100, $metaInfo->runParameters->application);
+        self::assertSame('2026-02-05', $metaInfo->runParameters->runDate->format('Y-m-d'));
+        self::assertSame('SC2139476-SC3', $metaInfo->runParameters->flowcell);
+        self::assertSame('2026-07-29', $metaInfo->runParameters->flowcellExpirationDate);
+        self::assertSame('', $metaInfo->runParameters->rta);
+        self::assertSame('1.1.0.26158', $metaInfo->runParameters->mcs);
+        self::assertSame('20260205_SH01038_0007_ASC2139476-SC3', $metaInfo->runParameters->info);
+
+        self::assertCount(2, $metaInfo->runParameters->reagents);
+        self::assertSame('SC2139476-SC3', $metaInfo->runParameters->reagents[0]['name']);
+        self::assertSame('2026-07-29', $metaInfo->runParameters->reagents[0]['expire_date']);
+        self::assertSame('SC2157208-SC2', $metaInfo->runParameters->reagents[1]['name']);
+        self::assertSame('2026-10-17', $metaInfo->runParameters->reagents[1]['expire_date']);
+
+        self::assertSame(1000.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->value);
+        self::assertSame(62.27, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterPF->value);
+        self::assertSame(95.35, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->q30);
+        self::assertSame(0.075, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->phasing);
+        self::assertSame(0.042, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->prephasing);
+        self::assertSame(28.66, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->aligned->value);
+        self::assertSame(0.27, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->error->value);
+        self::assertSame(3534, $metaInfo->interOpResult->resultsForRead1->intensityCycle);
+        self::assertSame(1490000, $metaInfo->interOpResult->resultsForRead1->yield);
+
+        self::assertSame(96.32, $metaInfo->interOpResult->resultsForRead2->sequencingQualityControl->q30);
+        self::assertSame(3486, $metaInfo->interOpResult->resultsForRead2->intensityCycle);
+        self::assertSame(1490000, $metaInfo->interOpResult->resultsForRead2->yield);
+
+        self::assertSame('mllsrv20/miseq_active\\miSeqi100\\20260205_SH01038_0007_ASC2139476-SC3\\meta-info.json', $metaInfo->uncPath);
+    }
+}

From 029de10b6b610a2a0f3abb9cfba4e45f4bafaa05 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 11:18:00 +0200
Subject: [PATCH 03/25] feat: implement interop

---
 src/InterOp/InterOpResult.php  |  4 ++--
 src/InterOp/LaneResult.php     | 14 +++++++-------
 src/InterOp/RunParameters.php  |  4 ++--
 tests/InterOp/MetaInfoTest.php |  5 ++---
 4 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index e697441..5cbe4cb 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -23,12 +23,12 @@ public function __construct(array $summary, array $reads)
 
         $read1Rows = $reads[$firstDataRead] ?? null;
         if ($read1Rows === null) {
-            throw new InterOpException("Reads data missing for '{$firstDataRead}'.");
+            throw new InterOpException("Reads data missing for: {$firstDataRead}.");
         }
 
         $read2Rows = $reads[$lastDataRead] ?? null;
         if ($read2Rows === null) {
-            throw new InterOpException("Reads data missing for '{$lastDataRead}'.");
+            throw new InterOpException("Reads data missing for: {$lastDataRead}.");
         }
 
         $this->resultsForRead1 = LaneResult::fromInterOpRow($read1Rows[0]);
diff --git a/src/InterOp/LaneResult.php b/src/InterOp/LaneResult.php
index 08b8c7d..bba9afc 100644
--- a/src/InterOp/LaneResult.php
+++ b/src/InterOp/LaneResult.php
@@ -32,23 +32,23 @@ public function __construct(ClusterStatistic $clusterStatistic, SequencingQualit
     public static function fromInterOpRow(array $row): self
     {
         $density = DeviationValue::parse($row['Density']);
-        assert($density instanceof DeviationValue, "Expected parseable Density, got: {$row['Density']}");
+        assert($density instanceof DeviationValue, "Expected parseable Density, got: {$row['Density']}.");
 
         $clusterPF = DeviationValue::parse($row['Cluster PF']);
-        assert($clusterPF instanceof DeviationValue, "Expected parseable Cluster PF, got: {$row['Cluster PF']}");
+        assert($clusterPF instanceof DeviationValue, "Expected parseable Cluster PF, got: {$row['Cluster PF']}.");
 
         $aligned = DeviationValue::parse($row['Aligned']);
-        assert($aligned instanceof DeviationValue, "Expected parseable Aligned, got: {$row['Aligned']}");
+        assert($aligned instanceof DeviationValue, "Expected parseable Aligned, got: {$row['Aligned']}.");
 
         $error = DeviationValue::parse($row['Error']);
-        assert($error instanceof DeviationValue, "Expected parseable Error, got: {$row['Error']}");
+        assert($error instanceof DeviationValue, "Expected parseable Error, got: {$row['Error']}.");
 
         $intensityCycle = DeviationValue::parse($row['Intensity C1']);
-        assert($intensityCycle instanceof DeviationValue, "Expected parseable Intensity C1, got: {$row['Intensity C1']}");
+        assert($intensityCycle instanceof DeviationValue, "Expected parseable Intensity C1, got: {$row['Intensity C1']}.");
 
         $phasingParts = explode(' / ', $row['Legacy Phasing/Prephasing Rate']);
-        assert(count($phasingParts) === 2, "Expected 'phasing / prephasing' format, got: {$row['Legacy Phasing/Prephasing Rate']}");
-        assert($phasingParts[0] !== 'nan', 'Unexpected nan phasing rate for data read');
+        assert(count($phasingParts) === 2, "Expected 'phasing / prephasing' format, got: {$row['Legacy Phasing/Prephasing Rate']}.");
+        assert($phasingParts[0] !== 'nan', 'Unexpected nan phasing rate for data read.');
 
         $clusterStatistic = new ClusterStatistic(
             $density,
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index 0eaf4d1..f7f9839 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -61,7 +61,7 @@ private function parseMiSeq(array $params): void
 
         $runStartDate = (string) $params['RunStartDate'];
         $date = Carbon::createFromFormat('!ymd', $runStartDate);
-        assert($date instanceof Carbon, "Failed to parse MiSeq RunStartDate: {$runStartDate}");
+        assert($date instanceof Carbon, "Failed to parse MiSeq RunStartDate: {$runStartDate}.");
         $this->runDate = $date;
 
         $this->flowcell = $this->stripZeroPrefix($params['FlowcellRFIDTag']['SerialNumber']);
@@ -95,7 +95,7 @@ private function parseMiSeqI100(array $params): void
         $runID = $params['RunId'];
         $dateString = substr($runID, 0, 8);
         $date = Carbon::createFromFormat('!Ymd', $dateString);
-        assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$runID}");
+        assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$runID}.");
         $this->runDate = $date;
 
         $consumables = $params['ConsumableInfo']['ConsumableInfo'];
diff --git a/tests/InterOp/MetaInfoTest.php b/tests/InterOp/MetaInfoTest.php
index 145de60..b20603a 100644
--- a/tests/InterOp/MetaInfoTest.php
+++ b/tests/InterOp/MetaInfoTest.php
@@ -3,7 +3,6 @@
 namespace MLL\Utils\Tests\InterOp;
 
 use MLL\Utils\InterOp\MetaInfo;
-use MLL\Utils\InterOp\RunParameters;
 use PHPUnit\Framework\TestCase;
 
 use function Safe\file_get_contents;
@@ -15,7 +14,7 @@ public function testParseMiSeq(): void
         $json = file_get_contents(__DIR__ . '/meta-info-miseq.json');
         $metaInfo = new MetaInfo($json);
 
-        self::assertSame(RunParameters::APPLICATION_MISEQ, $metaInfo->runParameters->application);
+        self::assertSame('MiSeq Control Software', $metaInfo->runParameters->application);
         self::assertSame('2023-04-21', $metaInfo->runParameters->runDate->format('Y-m-d'));
         self::assertSame('KT6CY', $metaInfo->runParameters->flowcell);
         self::assertSame('2023-09-27', $metaInfo->runParameters->flowcellExpirationDate);
@@ -60,7 +59,7 @@ public function testParseMiSeqI100(): void
         $json = file_get_contents(__DIR__ . '/meta-info-i100.json');
         $metaInfo = new MetaInfo($json);
 
-        self::assertSame(RunParameters::APPLICATION_MISEQ_I100, $metaInfo->runParameters->application);
+        self::assertSame('MiSeqi100Series Control Software', $metaInfo->runParameters->application);
         self::assertSame('2026-02-05', $metaInfo->runParameters->runDate->format('Y-m-d'));
         self::assertSame('SC2139476-SC3', $metaInfo->runParameters->flowcell);
         self::assertSame('2026-07-29', $metaInfo->runParameters->flowcellExpirationDate);

From d245f5514577a87acfaa87c044dcd2a0a979ee88 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 14:41:56 +0200
Subject: [PATCH 04/25] Claude review

---
 src/InterOp/ClusterStatistic.php         | 12 ++--
 src/InterOp/DeviationValue.php           | 21 ++++--
 src/InterOp/InterOpResult.php            | 28 ++++----
 src/InterOp/LaneResult.php               | 88 +++++++++---------------
 src/InterOp/MetaInfo.php                 | 20 ++++--
 src/InterOp/RunParameters.php            | 46 +++++--------
 src/InterOp/RunResult.php                |  6 +-
 src/InterOp/SequencingQualityControl.php | 15 ++--
 tests/InterOp/MetaInfoTest.php           |  6 +-
 tests/InterOp/meta-info-i100.json        |  6 +-
 tests/InterOp/meta-info-miseq.json       |  4 +-
 11 files changed, 116 insertions(+), 136 deletions(-)

diff --git a/src/InterOp/ClusterStatistic.php b/src/InterOp/ClusterStatistic.php
index 2876f51..7e01f53 100644
--- a/src/InterOp/ClusterStatistic.php
+++ b/src/InterOp/ClusterStatistic.php
@@ -4,17 +4,13 @@
 
 class ClusterStatistic
 {
-    /** @var DeviationValue Cluster density (K/mm²). */
-    public $density;
+    public DeviationValue $density;
 
-    /** @var DeviationValue Percentage of clusters passing filter. */
-    public $clusterPF;
+    public DeviationValue $clusterPF;
 
-    /** @var float Total cluster count (millions). */
-    public $clusterCount;
+    public float $clusterCount;
 
-    /** @var float Clusters passing filter (millions). */
-    public $clusterCountPF;
+    public float $clusterCountPF;
 
     public function __construct(DeviationValue $density, DeviationValue $clusterPF, float $clusterCount, float $clusterCountPF)
     {
diff --git a/src/InterOp/DeviationValue.php b/src/InterOp/DeviationValue.php
index 0167d2c..91131d2 100644
--- a/src/InterOp/DeviationValue.php
+++ b/src/InterOp/DeviationValue.php
@@ -2,15 +2,15 @@
 
 namespace MLL\Utils\InterOp;
 
+use MLL\Utils\SafeCast;
+
 use function Safe\preg_match;
 
 class DeviationValue
 {
-    /** @var float */
-    public $value;
+    public float $value;
 
-    /** @var float */
-    public $deviation;
+    public float $deviation;
 
     public function __construct(float $value, float $deviation)
     {
@@ -29,6 +29,17 @@ public static function parse(string $raw): ?self
             return null;
         }
 
-        return new self((float) $matches[1], (float) $matches[2]);
+        return new self(
+            SafeCast::toFloat($matches[1]),
+            SafeCast::toFloat($matches[2])
+        );
+    }
+
+    public static function average(self $a, self $b): self
+    {
+        return new self(
+            ($a->value + $b->value) / 2,
+            ($a->deviation + $b->deviation) / 2
+        );
     }
 }
diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index 5cbe4cb..ddaab8c 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -4,14 +4,11 @@
 
 class InterOpResult
 {
-    /** @var LaneResult */
-    public $resultsForRead1;
+    public LaneResult $resultsForRead1;
 
-    /** @var LaneResult */
-    public $resultsForRead2;
+    public LaneResult $resultsForRead2;
 
-    /** @var RunResult */
-    public $resultsForRun;
+    public RunResult $resultsForRun;
 
     /**
      * @param array<int, array<string, string>> $summary interop summary rows
@@ -22,15 +19,16 @@ public function __construct(array $summary, array $reads)
         [$firstDataRead, $lastDataRead] = self::findDataReads($summary);
 
         $read1Rows = $reads[$firstDataRead] ?? null;
-        if ($read1Rows === null) {
-            throw new InterOpException("Reads data missing for: {$firstDataRead}.");
+        if ($read1Rows === null || $read1Rows === []) {
+            throw new InterOpException("Reads data missing or empty for: {$firstDataRead}.");
         }
 
         $read2Rows = $reads[$lastDataRead] ?? null;
-        if ($read2Rows === null) {
-            throw new InterOpException("Reads data missing for: {$lastDataRead}.");
+        if ($read2Rows === null || $read2Rows === []) {
+            throw new InterOpException("Reads data missing or empty for: {$lastDataRead}.");
         }
 
+        // First row per read key is the Surface "-" aggregate across all tiles
         $this->resultsForRead1 = LaneResult::fromInterOpRow($read1Rows[0]);
         $this->resultsForRead2 = LaneResult::fromInterOpRow($read2Rows[0]);
         $this->resultsForRun = RunResult::fromLaneResults($this->resultsForRead1, $this->resultsForRead2);
@@ -64,10 +62,14 @@ public static function findDataReads(array $summary): array
             }
         }
 
-        if (count($dataReads) < 2) {
-            throw new InterOpException('Expected at least 2 data reads, found ' . count($dataReads) . '.');
+        $count = count($dataReads);
+        if ($count < 2) {
+            throw new InterOpException("Expected at least 2 data reads, found {$count}.");
         }
 
-        return [$dataReads[0], $dataReads[count($dataReads) - 1]];
+        $lastKey = array_key_last($dataReads);
+        assert($lastKey !== null, 'array_key_last() returned null despite count >= 2.');
+
+        return [$dataReads[0], $dataReads[$lastKey]];
     }
 }
diff --git a/src/InterOp/LaneResult.php b/src/InterOp/LaneResult.php
index bba9afc..60f580e 100644
--- a/src/InterOp/LaneResult.php
+++ b/src/InterOp/LaneResult.php
@@ -2,19 +2,18 @@
 
 namespace MLL\Utils\InterOp;
 
+use MLL\Utils\SafeCast;
+
 class LaneResult
 {
-    /** @var ClusterStatistic */
-    public $clusterStatistic;
+    public ClusterStatistic $clusterStatistic;
 
-    /** @var SequencingQualityControl */
-    public $sequencingQualityControl;
+    public SequencingQualityControl $sequencingQualityControl;
 
-    /** @var int Intensity at cycle 1. */
-    public $intensityCycle;
+    public int $intensityCycle;
 
-    /** @var int Yield in bases (JSON float in gigabases * 1_000_000). */
-    public $yield;
+    /** Yield in kilobases (JSON float in gigabases * 1_000_000). */
+    public int $yield;
 
     public function __construct(ClusterStatistic $clusterStatistic, SequencingQualityControl $sequencingQualityControl, int $intensityCycle, int $yield)
     {
@@ -49,72 +48,53 @@ public static function fromInterOpRow(array $row): self
         $phasingParts = explode(' / ', $row['Legacy Phasing/Prephasing Rate']);
         assert(count($phasingParts) === 2, "Expected 'phasing / prephasing' format, got: {$row['Legacy Phasing/Prephasing Rate']}.");
         assert($phasingParts[0] !== 'nan', 'Unexpected nan phasing rate for data read.');
+        assert($phasingParts[1] !== 'nan', 'Unexpected nan prephasing rate for data read.');
 
         $clusterStatistic = new ClusterStatistic(
-            $density,
-            $clusterPF,
-            (float) $row['Reads'],
-            (float) $row['Reads PF']
+            density: $density,
+            clusterPF: $clusterPF,
+            clusterCount: SafeCast::toFloat($row['Reads']),
+            clusterCountPF: SafeCast::toFloat($row['Reads PF'])
         );
 
         $sequencingQualityControl = new SequencingQualityControl(
-            (float) $row['%>=Q30'],
-            (float) $phasingParts[0],
-            (float) $phasingParts[1],
-            $aligned,
-            $error
+            q30: SafeCast::toFloat($row['%>=Q30']),
+            phasing: SafeCast::toFloat($phasingParts[0]),
+            prephasing: SafeCast::toFloat($phasingParts[1]),
+            aligned: $aligned,
+            error: $error
         );
 
         return new self(
-            $clusterStatistic,
-            $sequencingQualityControl,
-            (int) $intensityCycle->value,
-            (int) ((float) $row['Yield'] * 1000000)
+            clusterStatistic: $clusterStatistic,
+            sequencingQualityControl: $sequencingQualityControl,
+            intensityCycle: SafeCast::toInt($intensityCycle->value),
+            yield: SafeCast::toInt(SafeCast::toFloat($row['Yield']) * 1000000)
         );
     }
 
     public static function aggregate(self $a, self $b): self
     {
-        $density = new DeviationValue(
-            ($a->clusterStatistic->density->value + $b->clusterStatistic->density->value) / 2,
-            ($a->clusterStatistic->density->deviation + $b->clusterStatistic->density->deviation) / 2
-        );
-
-        $clusterPF = new DeviationValue(
-            ($a->clusterStatistic->clusterPF->value + $b->clusterStatistic->clusterPF->value) / 2,
-            ($a->clusterStatistic->clusterPF->deviation + $b->clusterStatistic->clusterPF->deviation) / 2
-        );
-
         $clusterStatistic = new ClusterStatistic(
-            $density,
-            $clusterPF,
-            $a->clusterStatistic->clusterCount + $b->clusterStatistic->clusterCount,
-            $a->clusterStatistic->clusterCountPF + $b->clusterStatistic->clusterCountPF
-        );
-
-        $aligned = new DeviationValue(
-            ($a->sequencingQualityControl->aligned->value + $b->sequencingQualityControl->aligned->value) / 2,
-            ($a->sequencingQualityControl->aligned->deviation + $b->sequencingQualityControl->aligned->deviation) / 2
-        );
-
-        $error = new DeviationValue(
-            ($a->sequencingQualityControl->error->value + $b->sequencingQualityControl->error->value) / 2,
-            ($a->sequencingQualityControl->error->deviation + $b->sequencingQualityControl->error->deviation) / 2
+            density: DeviationValue::average($a->clusterStatistic->density, $b->clusterStatistic->density),
+            clusterPF: DeviationValue::average($a->clusterStatistic->clusterPF, $b->clusterStatistic->clusterPF),
+            clusterCount: $a->clusterStatistic->clusterCount + $b->clusterStatistic->clusterCount,
+            clusterCountPF: $a->clusterStatistic->clusterCountPF + $b->clusterStatistic->clusterCountPF
         );
 
         $sequencingQualityControl = new SequencingQualityControl(
-            ($a->sequencingQualityControl->q30 + $b->sequencingQualityControl->q30) / 2,
-            ($a->sequencingQualityControl->phasing + $b->sequencingQualityControl->phasing) / 2,
-            ($a->sequencingQualityControl->prephasing + $b->sequencingQualityControl->prephasing) / 2,
-            $aligned,
-            $error
+            q30: ($a->sequencingQualityControl->q30 + $b->sequencingQualityControl->q30) / 2,
+            phasing: ($a->sequencingQualityControl->phasing + $b->sequencingQualityControl->phasing) / 2,
+            prephasing: ($a->sequencingQualityControl->prephasing + $b->sequencingQualityControl->prephasing) / 2,
+            aligned: DeviationValue::average($a->sequencingQualityControl->aligned, $b->sequencingQualityControl->aligned),
+            error: DeviationValue::average($a->sequencingQualityControl->error, $b->sequencingQualityControl->error)
         );
 
         return new self(
-            $clusterStatistic,
-            $sequencingQualityControl,
-            (int) (($a->intensityCycle + $b->intensityCycle) / 2),
-            $a->yield + $b->yield
+            clusterStatistic: $clusterStatistic,
+            sequencingQualityControl: $sequencingQualityControl,
+            intensityCycle: intdiv($a->intensityCycle + $b->intensityCycle, 2),
+            yield: $a->yield + $b->yield
         );
     }
 }
diff --git a/src/InterOp/MetaInfo.php b/src/InterOp/MetaInfo.php
index ef5ec8a..d866bf0 100644
--- a/src/InterOp/MetaInfo.php
+++ b/src/InterOp/MetaInfo.php
@@ -10,18 +10,24 @@
  */
 class MetaInfo
 {
-    /** @var RunParameters */
-    public $runParameters;
+    public RunParameters $runParameters;
 
-    /** @var InterOpResult */
-    public $interOpResult;
+    public InterOpResult $interOpResult;
 
-    /** @var string */
-    public $uncPath;
+    public string $uncPath;
 
     public function __construct(string $json)
     {
-        /** @var array{runParameters: array{RunParameters: MiSeqParams|I100Params}, interop: array{summary: array<int, array<string, string>>, reads: array<string, array<int, array<string, string>>>}, uncPath: string} $data */
+        /**
+         * @var array{
+         *     runParameters: array{RunParameters: MiSeqParams|I100Params},
+         *     interop: array{
+         *         summary: array<int, array<string, string>>,
+         *         reads: array<string, array<int, array<string, string>>>,
+         *     },
+         *     uncPath: string,
+         * } $data
+         */
         $data = json_decode($json, true);
 
         $this->runParameters = new RunParameters($data['runParameters']['RunParameters']);
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index f7f9839..46daef8 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -15,29 +15,22 @@ class RunParameters
     public const APPLICATION_MISEQ = 'MiSeq Control Software';
     public const APPLICATION_MISEQ_I100 = 'MiSeqi100Series Control Software';
 
-    /** @var string */
-    public $application;
+    public string $application;
 
-    /** @var Carbon */
-    public $runDate;
+    public Carbon $runDate;
 
-    /** @var string */
-    public $flowcell;
+    public string $flowcell;
 
-    /** @var string */
-    public $flowcellExpirationDate;
+    public ?string $flowcellExpirationDate = null;
 
-    /** @var string */
-    public $rta;
+    public ?string $rta = null;
 
-    /** @var string RunID / RunId. */
-    public $info;
+    public string $info;
 
-    /** @var string MCS / system suite version. */
-    public $mcs;
+    public string $mcs;
 
     /** @var array<int, array{name: string, expire_date: string}> */
-    public $reagents;
+    public array $reagents;
 
     /** @param MiSeqParams|I100Params $params */
     public function __construct(array $params)
@@ -90,29 +83,21 @@ private function parseMiSeqI100(array $params): void
         $this->application = $params['Application'];
         $this->info = $params['RunId'];
         $this->mcs = $params['SystemSuiteVersion'];
-        $this->rta = '';
+        $this->rta = null;
 
-        $runID = $params['RunId'];
-        $dateString = substr($runID, 0, 8);
+        $dateString = substr($this->info, 0, 8);
         $date = Carbon::createFromFormat('!Ymd', $dateString);
-        assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$runID}.");
+        assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$this->info}.");
         $this->runDate = $date;
 
         $consumables = $params['ConsumableInfo']['ConsumableInfo'];
         $this->flowcell = '';
-        $this->flowcellExpirationDate = '';
+        $this->flowcellExpirationDate = null;
         $this->reagents = [];
 
         foreach ($consumables as $consumable) {
             $type = $consumable['Type'];
 
-            if ($type === 'DryCartridge') {
-                $this->flowcell = $consumable['SerialNumber'];
-                if (isset($consumable['ExpirationDate'])) {
-                    $this->flowcellExpirationDate = $this->formatExpirationDate($consumable['ExpirationDate']);
-                }
-            }
-
             if ($type === 'DryCartridge' || $type === 'WetCartridge') {
                 $this->reagents[] = [
                     'name' => $consumable['SerialNumber'],
@@ -120,6 +105,13 @@ private function parseMiSeqI100(array $params): void
                         ? $this->formatExpirationDate($consumable['ExpirationDate'])
                         : '',
                 ];
+
+                if ($type === 'DryCartridge') {
+                    $this->flowcell = $consumable['SerialNumber'];
+                    if (isset($consumable['ExpirationDate'])) {
+                        $this->flowcellExpirationDate = $this->formatExpirationDate($consumable['ExpirationDate']);
+                    }
+                }
             }
         }
     }
diff --git a/src/InterOp/RunResult.php b/src/InterOp/RunResult.php
index a496dff..f8e4d69 100644
--- a/src/InterOp/RunResult.php
+++ b/src/InterOp/RunResult.php
@@ -4,11 +4,9 @@
 
 class RunResult
 {
-    /** @var ClusterStatistic */
-    public $clusterStatistic;
+    public ClusterStatistic $clusterStatistic;
 
-    /** @var SequencingQualityControl */
-    public $sequencingQualityControl;
+    public SequencingQualityControl $sequencingQualityControl;
 
     public function __construct(ClusterStatistic $clusterStatistic, SequencingQualityControl $sequencingQualityControl)
     {
diff --git a/src/InterOp/SequencingQualityControl.php b/src/InterOp/SequencingQualityControl.php
index 52b8389..056c314 100644
--- a/src/InterOp/SequencingQualityControl.php
+++ b/src/InterOp/SequencingQualityControl.php
@@ -4,20 +4,15 @@
 
 class SequencingQualityControl
 {
-    /** @var float Percentage of bases with quality score >= Q30. */
-    public $q30;
+    public float $q30;
 
-    /** @var float Phasing rate. */
-    public $phasing;
+    public float $phasing;
 
-    /** @var float Prephasing rate. */
-    public $prephasing;
+    public float $prephasing;
 
-    /** @var DeviationValue Alignment percentage. */
-    public $aligned;
+    public DeviationValue $aligned;
 
-    /** @var DeviationValue Error rate. */
-    public $error;
+    public DeviationValue $error;
 
     public function __construct(float $q30, float $phasing, float $prephasing, DeviationValue $aligned, DeviationValue $error)
     {
diff --git a/tests/InterOp/MetaInfoTest.php b/tests/InterOp/MetaInfoTest.php
index b20603a..6f9c17f 100644
--- a/tests/InterOp/MetaInfoTest.php
+++ b/tests/InterOp/MetaInfoTest.php
@@ -51,7 +51,7 @@ public function testParseMiSeq(): void
         self::assertEqualsWithDelta(83.195, $runQC->q30, 0.001);
         self::assertEqualsWithDelta(0.065, $runQC->phasing, 0.001);
 
-        self::assertSame('mllsrv20/miseq_active\\230421_M02074_0859_000000000-KT6CY\\meta-info.json', $metaInfo->uncPath);
+        self::assertSame('example-server/miseq_active\\230421_M02074_0859_000000000-KT6CY\\meta-info.json', $metaInfo->uncPath);
     }
 
     public function testParseMiSeqI100(): void
@@ -63,7 +63,7 @@ public function testParseMiSeqI100(): void
         self::assertSame('2026-02-05', $metaInfo->runParameters->runDate->format('Y-m-d'));
         self::assertSame('SC2139476-SC3', $metaInfo->runParameters->flowcell);
         self::assertSame('2026-07-29', $metaInfo->runParameters->flowcellExpirationDate);
-        self::assertSame('', $metaInfo->runParameters->rta);
+        self::assertNull($metaInfo->runParameters->rta);
         self::assertSame('1.1.0.26158', $metaInfo->runParameters->mcs);
         self::assertSame('20260205_SH01038_0007_ASC2139476-SC3', $metaInfo->runParameters->info);
 
@@ -87,6 +87,6 @@ public function testParseMiSeqI100(): void
         self::assertSame(3486, $metaInfo->interOpResult->resultsForRead2->intensityCycle);
         self::assertSame(1490000, $metaInfo->interOpResult->resultsForRead2->yield);
 
-        self::assertSame('mllsrv20/miseq_active\\miSeqi100\\20260205_SH01038_0007_ASC2139476-SC3\\meta-info.json', $metaInfo->uncPath);
+        self::assertSame('example-server/miseq_active\\miSeqi100\\20260205_SH01038_0007_ASC2139476-SC3\\meta-info.json', $metaInfo->uncPath);
     }
 }
diff --git a/tests/InterOp/meta-info-i100.json b/tests/InterOp/meta-info-i100.json
index a7fc762..fc23d26 100644
--- a/tests/InterOp/meta-info-i100.json
+++ b/tests/InterOp/meta-info-i100.json
@@ -9,7 +9,7 @@
       "@xmlns:xsd": "http://www.w3.org/2001/XMLSchema",
       "Application": "MiSeqi100Series Control Software",
       "SystemSuiteVersion": "1.1.0.26158",
-      "OutputFolder": "//192.168.0.228/miseq_active/miSeqi100/20260205_SH01038_0007_ASC2139476-SC3",
+      "OutputFolder": "//192.0.2.1/miseq_active/miSeqi100/20260205_SH01038_0007_ASC2139476-SC3",
       "CustomPrimerSelections": {
         "ReadOnePrimer": false,
         "ReadTwoPrimer": false,
@@ -252,5 +252,5 @@
       ]
     }
   },
-  "uncPath": "mllsrv20/miseq_active\\miSeqi100\\20260205_SH01038_0007_ASC2139476-SC3\\meta-info.json"
-}
\ No newline at end of file
+  "uncPath": "example-server/miseq_active\\miSeqi100\\20260205_SH01038_0007_ASC2139476-SC3\\meta-info.json"
+}
diff --git a/tests/InterOp/meta-info-miseq.json b/tests/InterOp/meta-info-miseq.json
index d69b8e0..6d210d3 100644
--- a/tests/InterOp/meta-info-miseq.json
+++ b/tests/InterOp/meta-info-miseq.json
@@ -356,5 +356,5 @@
       ]
     }
   },
-  "uncPath": "mllsrv20/miseq_active\\230421_M02074_0859_000000000-KT6CY\\meta-info.json"
-}
\ No newline at end of file
+  "uncPath": "example-server/miseq_active\\230421_M02074_0859_000000000-KT6CY\\meta-info.json"
+}

From e05a7820c87f2e8e2c0fe53a0efcaf908265ed68 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 14:42:01 +0200
Subject: [PATCH 05/25] Claude review

---
 tests/InterOp/DeviationValueTest.php | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/InterOp/DeviationValueTest.php b/tests/InterOp/DeviationValueTest.php
index e1eaf79..84da30f 100644
--- a/tests/InterOp/DeviationValueTest.php
+++ b/tests/InterOp/DeviationValueTest.php
@@ -25,12 +25,12 @@ public function testParse(string $input, ?float $expectedValue, ?float $expected
         self::assertSame($expectedDeviation, $result->deviation);
     }
 
-    /** @return iterable<string, array{string, float|null, float|null}> */
+    /** @return iterable<string, array{input: string, expectedValue: float|null, expectedDeviation: float|null}> */
     public static function parseProvider(): iterable
     {
-        yield 'integer values' => ['851 +/- 32', 851.0, 32.0];
-        yield 'decimal values' => ['96.54 +/- 0.25', 96.54, 0.25];
-        yield 'nan returns null' => ['nan +/- nan', null, null];
-        yield 'small decimal values' => ['0.085 +/- 0.020', 0.085, 0.02];
+        yield 'integer values' => ['input' => '851 +/- 32', 'expectedValue' => 851.0, 'expectedDeviation' => 32.0];
+        yield 'decimal values' => ['input' => '96.54 +/- 0.25', 'expectedValue' => 96.54, 'expectedDeviation' => 0.25];
+        yield 'nan returns null' => ['input' => 'nan +/- nan', 'expectedValue' => null, 'expectedDeviation' => null];
+        yield 'small decimal values' => ['input' => '0.085 +/- 0.020', 'expectedValue' => 0.085, 'expectedDeviation' => 0.02];
     }
 }

From 3c47bf548360c75abb73c5e9ce6987aa79553ed6 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 15:05:40 +0200
Subject: [PATCH 06/25] Claude review

---
 tests/InterOp/InterOpResultTest.php | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/tests/InterOp/InterOpResultTest.php b/tests/InterOp/InterOpResultTest.php
index 09b6559..f917557 100644
--- a/tests/InterOp/InterOpResultTest.php
+++ b/tests/InterOp/InterOpResultTest.php
@@ -22,25 +22,25 @@ public function testFindDataReads(string $description, array $summary, string $e
         self::assertSame($expectedLast, $last, "{$description}: last data read");
     }
 
-    /** @return iterable<string, array{string, array<int, array<string, string>>, string, string}> */
+    /** @return iterable<string, array{description: string, summary: array<int, array<string, string>>, expectedFirst: string, expectedLast: string}> */
     public static function dataReadDetectionProvider(): iterable
     {
         yield 'MiSeq single-index' => [
-            'MiSeq with one index read',
-            [
+            'description' => 'MiSeq with one index read',
+            'summary' => [
                 ['Level' => 'Read 1'],
                 ['Level' => 'Read 2 (I)'],
                 ['Level' => 'Read 3'],
                 ['Level' => 'Non-indexed'],
                 ['Level' => 'Total'],
             ],
-            'Read 1',
-            'Read 3',
+            'expectedFirst' => 'Read 1',
+            'expectedLast' => 'Read 3',
         ];
 
         yield 'MiSeq dual-index' => [
-            'MiSeq with two index reads',
-            [
+            'description' => 'MiSeq with two index reads',
+            'summary' => [
                 ['Level' => 'Read 1'],
                 ['Level' => 'Read 2 (I)'],
                 ['Level' => 'Read 3 (I)'],
@@ -48,13 +48,13 @@ public static function dataReadDetectionProvider(): iterable
                 ['Level' => 'Non-indexed'],
                 ['Level' => 'Total'],
             ],
-            'Read 1',
-            'Read 4',
+            'expectedFirst' => 'Read 1',
+            'expectedLast' => 'Read 4',
         ];
 
         yield 'i100 dual-index' => [
-            'i100 with index reads first',
-            [
+            'description' => 'i100 with index reads first',
+            'summary' => [
                 ['Level' => 'Read 1 (I)'],
                 ['Level' => 'Read 2 (I)'],
                 ['Level' => 'Read 3'],
@@ -62,8 +62,8 @@ public static function dataReadDetectionProvider(): iterable
                 ['Level' => 'Non-indexed'],
                 ['Level' => 'Total'],
             ],
-            'Read 3',
-            'Read 4',
+            'expectedFirst' => 'Read 3',
+            'expectedLast' => 'Read 4',
         ];
     }
 }

From 3eac2ab6fadf2578cc7eff393fab8e998078b955 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 17:11:49 +0200
Subject: [PATCH 07/25] Update shortcuts use fully names

---
 src/InterOp/ClusterStatistic.php | 10 +++++-----
 src/InterOp/LaneResult.php       | 12 ++++++------
 src/InterOp/RunParameters.php    | 12 ++++++------
 tests/InterOp/MetaInfoTest.php   | 14 +++++++-------
 4 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/src/InterOp/ClusterStatistic.php b/src/InterOp/ClusterStatistic.php
index 7e01f53..06b196e 100644
--- a/src/InterOp/ClusterStatistic.php
+++ b/src/InterOp/ClusterStatistic.php
@@ -6,17 +6,17 @@ class ClusterStatistic
 {
     public DeviationValue $density;
 
-    public DeviationValue $clusterPF;
+    public DeviationValue $clusterPassingFilter;
 
     public float $clusterCount;
 
-    public float $clusterCountPF;
+    public float $clusterCountPassingFilter;
 
-    public function __construct(DeviationValue $density, DeviationValue $clusterPF, float $clusterCount, float $clusterCountPF)
+    public function __construct(DeviationValue $density, DeviationValue $clusterPassingFilter, float $clusterCount, float $clusterCountPassingFilter)
     {
         $this->density = $density;
-        $this->clusterPF = $clusterPF;
+        $this->clusterPassingFilter = $clusterPassingFilter;
         $this->clusterCount = $clusterCount;
-        $this->clusterCountPF = $clusterCountPF;
+        $this->clusterCountPassingFilter = $clusterCountPassingFilter;
     }
 }
diff --git a/src/InterOp/LaneResult.php b/src/InterOp/LaneResult.php
index 60f580e..013b2b7 100644
--- a/src/InterOp/LaneResult.php
+++ b/src/InterOp/LaneResult.php
@@ -33,8 +33,8 @@ public static function fromInterOpRow(array $row): self
         $density = DeviationValue::parse($row['Density']);
         assert($density instanceof DeviationValue, "Expected parseable Density, got: {$row['Density']}.");
 
-        $clusterPF = DeviationValue::parse($row['Cluster PF']);
-        assert($clusterPF instanceof DeviationValue, "Expected parseable Cluster PF, got: {$row['Cluster PF']}.");
+        $clusterPassingFilter = DeviationValue::parse($row['Cluster PF']);
+        assert($clusterPassingFilter instanceof DeviationValue, "Expected parseable Cluster PF, got: {$row['Cluster PF']}.");
 
         $aligned = DeviationValue::parse($row['Aligned']);
         assert($aligned instanceof DeviationValue, "Expected parseable Aligned, got: {$row['Aligned']}.");
@@ -52,9 +52,9 @@ public static function fromInterOpRow(array $row): self
 
         $clusterStatistic = new ClusterStatistic(
             density: $density,
-            clusterPF: $clusterPF,
+            clusterPassingFilter: $clusterPassingFilter,
             clusterCount: SafeCast::toFloat($row['Reads']),
-            clusterCountPF: SafeCast::toFloat($row['Reads PF'])
+            clusterCountPassingFilter: SafeCast::toFloat($row['Reads PF'])
         );
 
         $sequencingQualityControl = new SequencingQualityControl(
@@ -77,9 +77,9 @@ public static function aggregate(self $a, self $b): self
     {
         $clusterStatistic = new ClusterStatistic(
             density: DeviationValue::average($a->clusterStatistic->density, $b->clusterStatistic->density),
-            clusterPF: DeviationValue::average($a->clusterStatistic->clusterPF, $b->clusterStatistic->clusterPF),
+            clusterPassingFilter: DeviationValue::average($a->clusterStatistic->clusterPassingFilter, $b->clusterStatistic->clusterPassingFilter),
             clusterCount: $a->clusterStatistic->clusterCount + $b->clusterStatistic->clusterCount,
-            clusterCountPF: $a->clusterStatistic->clusterCountPF + $b->clusterStatistic->clusterCountPF
+            clusterCountPassingFilter: $a->clusterStatistic->clusterCountPassingFilter + $b->clusterStatistic->clusterCountPassingFilter
         );
 
         $sequencingQualityControl = new SequencingQualityControl(
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index 46daef8..196c20a 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -23,11 +23,11 @@ class RunParameters
 
     public ?string $flowcellExpirationDate = null;
 
-    public ?string $rta = null;
+    public ?string $realTimeAnalysisVersion = null;
 
     public string $info;
 
-    public string $mcs;
+    public string $controlSoftwareVersion;
 
     /** @var array<int, array{name: string, expire_date: string}> */
     public array $reagents;
@@ -49,8 +49,8 @@ private function parseMiSeq(array $params): void
     {
         $this->application = $params['Setup']['ApplicationName'];
         $this->info = $params['RunID'];
-        $this->mcs = $params['MCSVersion'];
-        $this->rta = $params['RTAVersion'];
+        $this->controlSoftwareVersion = $params['MCSVersion'];
+        $this->realTimeAnalysisVersion = $params['RTAVersion'];
 
         $runStartDate = (string) $params['RunStartDate'];
         $date = Carbon::createFromFormat('!ymd', $runStartDate);
@@ -82,8 +82,8 @@ private function parseMiSeqI100(array $params): void
     {
         $this->application = $params['Application'];
         $this->info = $params['RunId'];
-        $this->mcs = $params['SystemSuiteVersion'];
-        $this->rta = null;
+        $this->controlSoftwareVersion = $params['SystemSuiteVersion'];
+        $this->realTimeAnalysisVersion = null;
 
         $dateString = substr($this->info, 0, 8);
         $date = Carbon::createFromFormat('!Ymd', $dateString);
diff --git a/tests/InterOp/MetaInfoTest.php b/tests/InterOp/MetaInfoTest.php
index 6f9c17f..db9a3ab 100644
--- a/tests/InterOp/MetaInfoTest.php
+++ b/tests/InterOp/MetaInfoTest.php
@@ -18,8 +18,8 @@ public function testParseMiSeq(): void
         self::assertSame('2023-04-21', $metaInfo->runParameters->runDate->format('Y-m-d'));
         self::assertSame('KT6CY', $metaInfo->runParameters->flowcell);
         self::assertSame('2023-09-27', $metaInfo->runParameters->flowcellExpirationDate);
-        self::assertSame('1.18.54', $metaInfo->runParameters->rta);
-        self::assertSame('2.6.2.2', $metaInfo->runParameters->mcs);
+        self::assertSame('1.18.54', $metaInfo->runParameters->realTimeAnalysisVersion);
+        self::assertSame('2.6.2.2', $metaInfo->runParameters->controlSoftwareVersion);
         self::assertSame('230421_M02074_0859_000000000-KT6CY', $metaInfo->runParameters->info);
 
         self::assertCount(2, $metaInfo->runParameters->reagents);
@@ -30,9 +30,9 @@ public function testParseMiSeq(): void
 
         self::assertSame(851.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->value);
         self::assertSame(32.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->deviation);
-        self::assertSame(96.54, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterPF->value);
+        self::assertSame(96.54, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterPassingFilter->value);
         self::assertSame(21.22, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCount);
-        self::assertSame(20.48, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCountPF);
+        self::assertSame(20.48, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCountPassingFilter);
 
         self::assertSame(88.2, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->q30);
         self::assertSame(0.085, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->phasing);
@@ -63,8 +63,8 @@ public function testParseMiSeqI100(): void
         self::assertSame('2026-02-05', $metaInfo->runParameters->runDate->format('Y-m-d'));
         self::assertSame('SC2139476-SC3', $metaInfo->runParameters->flowcell);
         self::assertSame('2026-07-29', $metaInfo->runParameters->flowcellExpirationDate);
-        self::assertNull($metaInfo->runParameters->rta);
-        self::assertSame('1.1.0.26158', $metaInfo->runParameters->mcs);
+        self::assertNull($metaInfo->runParameters->realTimeAnalysisVersion);
+        self::assertSame('1.1.0.26158', $metaInfo->runParameters->controlSoftwareVersion);
         self::assertSame('20260205_SH01038_0007_ASC2139476-SC3', $metaInfo->runParameters->info);
 
         self::assertCount(2, $metaInfo->runParameters->reagents);
@@ -74,7 +74,7 @@ public function testParseMiSeqI100(): void
         self::assertSame('2026-10-17', $metaInfo->runParameters->reagents[1]['expire_date']);
 
         self::assertSame(1000.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->value);
-        self::assertSame(62.27, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterPF->value);
+        self::assertSame(62.27, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterPassingFilter->value);
         self::assertSame(95.35, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->q30);
         self::assertSame(0.075, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->phasing);
         self::assertSame(0.042, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->prephasing);

From 1f8ecfa21e22a741524d98d61684baf1d30f8050 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 17:24:32 +0200
Subject: [PATCH 08/25] Multiline fix

---
 src/InterOp/RunParameters.php | 34 ++++++++++++++++++++++++++++++----
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index 196c20a..61b8090 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -5,10 +5,36 @@
 use Carbon\Carbon;
 
 /**
- * @phpstan-type RFIDTag array{SerialNumber: string, PartNumber: int, ExpirationDate: string}
- * @phpstan-type MiSeqParams array{Setup: array{ApplicationName: string}, RunID: string, MCSVersion: string, RTAVersion: string, RunStartDate: int, FlowcellRFIDTag: RFIDTag, PR2BottleRFIDTag?: RFIDTag, ReagentKitRFIDTag?: RFIDTag}
- * @phpstan-type Consumable array{SerialNumber: string, Type: string, ExpirationDate?: string, LotNumber?: int, PartNumber?: int, Mode?: string|int, Version?: int}
- * @phpstan-type I100Params array{Application: string, RunId: string, SystemSuiteVersion: string, ConsumableInfo: array{ConsumableInfo: array<int, Consumable>}}
+ * @phpstan-type RFIDTag array{
+ *     SerialNumber: string,
+ *     PartNumber: int,
+ *     ExpirationDate: string,
+ * }
+ * @phpstan-type MiSeqParams array{
+ *     Setup: array{ApplicationName: string},
+ *     RunID: string,
+ *     MCSVersion: string,
+ *     RTAVersion: string,
+ *     RunStartDate: int,
+ *     FlowcellRFIDTag: RFIDTag,
+ *     PR2BottleRFIDTag?: RFIDTag,
+ *     ReagentKitRFIDTag?: RFIDTag,
+ * }
+ * @phpstan-type Consumable array{
+ *     SerialNumber: string,
+ *     Type: string,
+ *     ExpirationDate?: string,
+ *     LotNumber?: int,
+ *     PartNumber?: int,
+ *     Mode?: string|int,
+ *     Version?: int,
+ * }
+ * @phpstan-type I100Params array{
+ *     Application: string,
+ *     RunId: string,
+ *     SystemSuiteVersion: string,
+ *     ConsumableInfo: array{ConsumableInfo: array<int, Consumable>},
+ * }
  */
 class RunParameters
 {

From 0c1e59ce45c2296e168ceac5e7a8ab2b96a3e639 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 17:33:33 +0200
Subject: [PATCH 09/25] Fix named arguments

---
 src/InterOp/LaneResult.php | 52 +++++++++++++++++++-------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/src/InterOp/LaneResult.php b/src/InterOp/LaneResult.php
index 013b2b7..8c2debf 100644
--- a/src/InterOp/LaneResult.php
+++ b/src/InterOp/LaneResult.php
@@ -51,50 +51,50 @@ public static function fromInterOpRow(array $row): self
         assert($phasingParts[1] !== 'nan', 'Unexpected nan prephasing rate for data read.');
 
         $clusterStatistic = new ClusterStatistic(
-            density: $density,
-            clusterPassingFilter: $clusterPassingFilter,
-            clusterCount: SafeCast::toFloat($row['Reads']),
-            clusterCountPassingFilter: SafeCast::toFloat($row['Reads PF'])
+            $density,
+            $clusterPassingFilter,
+            SafeCast::toFloat($row['Reads']),
+            SafeCast::toFloat($row['Reads PF'])
         );
 
         $sequencingQualityControl = new SequencingQualityControl(
-            q30: SafeCast::toFloat($row['%>=Q30']),
-            phasing: SafeCast::toFloat($phasingParts[0]),
-            prephasing: SafeCast::toFloat($phasingParts[1]),
-            aligned: $aligned,
-            error: $error
+            SafeCast::toFloat($row['%>=Q30']),
+            SafeCast::toFloat($phasingParts[0]),
+            SafeCast::toFloat($phasingParts[1]),
+            $aligned,
+            $error
         );
 
         return new self(
-            clusterStatistic: $clusterStatistic,
-            sequencingQualityControl: $sequencingQualityControl,
-            intensityCycle: SafeCast::toInt($intensityCycle->value),
-            yield: SafeCast::toInt(SafeCast::toFloat($row['Yield']) * 1000000)
+            $clusterStatistic,
+            $sequencingQualityControl,
+            SafeCast::toInt($intensityCycle->value),
+            SafeCast::toInt(SafeCast::toFloat($row['Yield']) * 1000000)
         );
     }
 
     public static function aggregate(self $a, self $b): self
     {
         $clusterStatistic = new ClusterStatistic(
-            density: DeviationValue::average($a->clusterStatistic->density, $b->clusterStatistic->density),
-            clusterPassingFilter: DeviationValue::average($a->clusterStatistic->clusterPassingFilter, $b->clusterStatistic->clusterPassingFilter),
-            clusterCount: $a->clusterStatistic->clusterCount + $b->clusterStatistic->clusterCount,
-            clusterCountPassingFilter: $a->clusterStatistic->clusterCountPassingFilter + $b->clusterStatistic->clusterCountPassingFilter
+            DeviationValue::average($a->clusterStatistic->density, $b->clusterStatistic->density),
+            DeviationValue::average($a->clusterStatistic->clusterPassingFilter, $b->clusterStatistic->clusterPassingFilter),
+            $a->clusterStatistic->clusterCount + $b->clusterStatistic->clusterCount,
+            $a->clusterStatistic->clusterCountPassingFilter + $b->clusterStatistic->clusterCountPassingFilter
         );
 
         $sequencingQualityControl = new SequencingQualityControl(
-            q30: ($a->sequencingQualityControl->q30 + $b->sequencingQualityControl->q30) / 2,
-            phasing: ($a->sequencingQualityControl->phasing + $b->sequencingQualityControl->phasing) / 2,
-            prephasing: ($a->sequencingQualityControl->prephasing + $b->sequencingQualityControl->prephasing) / 2,
-            aligned: DeviationValue::average($a->sequencingQualityControl->aligned, $b->sequencingQualityControl->aligned),
-            error: DeviationValue::average($a->sequencingQualityControl->error, $b->sequencingQualityControl->error)
+            ($a->sequencingQualityControl->q30 + $b->sequencingQualityControl->q30) / 2,
+            ($a->sequencingQualityControl->phasing + $b->sequencingQualityControl->phasing) / 2,
+            ($a->sequencingQualityControl->prephasing + $b->sequencingQualityControl->prephasing) / 2,
+            DeviationValue::average($a->sequencingQualityControl->aligned, $b->sequencingQualityControl->aligned),
+            DeviationValue::average($a->sequencingQualityControl->error, $b->sequencingQualityControl->error)
         );
 
         return new self(
-            clusterStatistic: $clusterStatistic,
-            sequencingQualityControl: $sequencingQualityControl,
-            intensityCycle: intdiv($a->intensityCycle + $b->intensityCycle, 2),
-            yield: $a->yield + $b->yield
+            $clusterStatistic,
+            $sequencingQualityControl,
+            intdiv($a->intensityCycle + $b->intensityCycle, 2),
+            $a->yield + $b->yield
         );
     }
 }

From 64d4ce65bbfb08ab17242f7f61eb845c3cb56ff9 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 17:43:47 +0200
Subject: [PATCH 10/25] Fix stan errors

---
 src/InterOp/InterOpResult.php | 2 +-
 src/InterOp/RunParameters.php | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index ddaab8c..a2967fd 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -57,7 +57,7 @@ public static function findDataReads(array $summary): array
                 continue;
             }
 
-            if (substr($level, -3) !== '(I)') {
+            if (substr($level, -3) !== '(I)') { // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
                 $dataReads[] = $level;
             }
         }
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index 61b8090..98e7803 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -111,7 +111,7 @@ private function parseMiSeqI100(array $params): void
         $this->controlSoftwareVersion = $params['SystemSuiteVersion'];
         $this->realTimeAnalysisVersion = null;
 
-        $dateString = substr($this->info, 0, 8);
+        $dateString = substr($this->info, 0, 8); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
         $date = Carbon::createFromFormat('!Ymd', $dateString);
         assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$this->info}.");
         $this->runDate = $date;
@@ -149,9 +149,9 @@ private function stripZeroPrefix(string $serial): string
             return $serial;
         }
 
-        $prefix = substr($serial, 0, $pos);
+        $prefix = substr($serial, 0, $pos); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
         if ($prefix !== '' && trim($prefix, '0') === '') {
-            return substr($serial, $pos + 1);
+            return substr($serial, $pos + 1); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
         }
 
         return $serial;

From 3c004573ac1694e71e2f1c807f191d86aeb832ce Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Fri, 24 Apr 2026 19:39:38 +0200
Subject: [PATCH 11/25] Fix stan errors

---
 src/InterOp/DeviationValue.php | 2 ++
 src/InterOp/InterOpResult.php  | 5 +----
 src/InterOp/RunParameters.php  | 2 +-
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/InterOp/DeviationValue.php b/src/InterOp/DeviationValue.php
index 91131d2..3ee2f1d 100644
--- a/src/InterOp/DeviationValue.php
+++ b/src/InterOp/DeviationValue.php
@@ -29,6 +29,8 @@ public static function parse(string $raw): ?self
             return null;
         }
 
+        assert(isset($matches[1], $matches[2]), "Regex matched but captures missing in: {$raw}.");
+
         return new self(
             SafeCast::toFloat($matches[1]),
             SafeCast::toFloat($matches[2])
diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index a2967fd..f9ec646 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -67,9 +67,6 @@ public static function findDataReads(array $summary): array
             throw new InterOpException("Expected at least 2 data reads, found {$count}.");
         }
 
-        $lastKey = array_key_last($dataReads);
-        assert($lastKey !== null, 'array_key_last() returned null despite count >= 2.');
-
-        return [$dataReads[0], $dataReads[$lastKey]];
+        return [$dataReads[0], $dataReads[count($dataReads) - 1]];
     }
 }
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index 98e7803..ae488da 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -63,7 +63,7 @@ public function __construct(array $params)
     {
         if (isset($params['Setup']['ApplicationName'])) {
             $this->parseMiSeq($params);
-        } elseif (isset($params['Application'])) {
+        } elseif (isset($params['Application'])) { // @phpstan-ignore isset.offset (runtime guard for unexpected input)
             $this->parseMiSeqI100($params);
         } else {
             throw new InterOpException('Unable to determine device type from RunParameters.');

From 032d8ba3914d081ca97cc00ae76b6ac767b99d8e Mon Sep 17 00:00:00 2001
From: Simon Bigelmayr <simon.bigelmayr@mll.com>
Date: Mon, 27 Apr 2026 12:16:17 +0200
Subject: [PATCH 12/25] fix: address review comments (no-brainer fixes)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Replace @phpstan-ignore-line with structured @phpstan-ignore form
- Change private methods to protected in library package
- Replace Carbon::parse() with Carbon::createFromFormat() for known formats
- Replace (string) cast with SafeCast::toString() + str_pad for pre-2010 dates
- Remove unreachable assert in DeviationValue::parse()
- Use existing $count variable instead of redundant count() call
- Extract duplicate formatExpirationDate() call in DryCartridge block

🤖 Generated with Claude Code
---
 src/InterOp/DeviationValue.php |  2 --
 src/InterOp/InterOpResult.php  |  4 ++--
 src/InterOp/RunParameters.php  | 44 ++++++++++++++++++++++------------
 3 files changed, 31 insertions(+), 19 deletions(-)

diff --git a/src/InterOp/DeviationValue.php b/src/InterOp/DeviationValue.php
index 3ee2f1d..91131d2 100644
--- a/src/InterOp/DeviationValue.php
+++ b/src/InterOp/DeviationValue.php
@@ -29,8 +29,6 @@ public static function parse(string $raw): ?self
             return null;
         }
 
-        assert(isset($matches[1], $matches[2]), "Regex matched but captures missing in: {$raw}.");
-
         return new self(
             SafeCast::toFloat($matches[1]),
             SafeCast::toFloat($matches[2])
diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index f9ec646..cf12515 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -57,7 +57,7 @@ public static function findDataReads(array $summary): array
                 continue;
             }
 
-            if (substr($level, -3) !== '(I)') { // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
+            if (substr($level, -3) !== '(I)') { // @phpstan-ignore theCodingMachineSafe.function (safe from PHP 8.0)
                 $dataReads[] = $level;
             }
         }
@@ -67,6 +67,6 @@ public static function findDataReads(array $summary): array
             throw new InterOpException("Expected at least 2 data reads, found {$count}.");
         }
 
-        return [$dataReads[0], $dataReads[count($dataReads) - 1]];
+        return [$dataReads[0], $dataReads[$count - 1]];
     }
 }
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index ae488da..abc7694 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -3,6 +3,7 @@
 namespace MLL\Utils\InterOp;
 
 use Carbon\Carbon;
+use MLL\Utils\SafeCast;
 
 /**
  * @phpstan-type RFIDTag array{
@@ -71,14 +72,14 @@ public function __construct(array $params)
     }
 
     /** @param MiSeqParams $params */
-    private function parseMiSeq(array $params): void
+    protected function parseMiSeq(array $params): void
     {
         $this->application = $params['Setup']['ApplicationName'];
         $this->info = $params['RunID'];
         $this->controlSoftwareVersion = $params['MCSVersion'];
         $this->realTimeAnalysisVersion = $params['RTAVersion'];
 
-        $runStartDate = (string) $params['RunStartDate'];
+        $runStartDate = str_pad(SafeCast::toString($params['RunStartDate']), 6, '0', STR_PAD_LEFT);
         $date = Carbon::createFromFormat('!ymd', $runStartDate);
         assert($date instanceof Carbon, "Failed to parse MiSeq RunStartDate: {$runStartDate}.");
         $this->runDate = $date;
@@ -104,14 +105,14 @@ private function parseMiSeq(array $params): void
     }
 
     /** @param I100Params $params */
-    private function parseMiSeqI100(array $params): void
+    protected function parseMiSeqI100(array $params): void
     {
         $this->application = $params['Application'];
         $this->info = $params['RunId'];
         $this->controlSoftwareVersion = $params['SystemSuiteVersion'];
         $this->realTimeAnalysisVersion = null;
 
-        $dateString = substr($this->info, 0, 8); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
+        $dateString = substr($this->info, 0, 8); // @phpstan-ignore theCodingMachineSafe.function (safe from PHP 8.0)
         $date = Carbon::createFromFormat('!Ymd', $dateString);
         assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$this->info}.");
         $this->runDate = $date;
@@ -125,42 +126,55 @@ private function parseMiSeqI100(array $params): void
             $type = $consumable['Type'];
 
             if ($type === 'DryCartridge' || $type === 'WetCartridge') {
+                $expireDate = isset($consumable['ExpirationDate'])
+                    ? $this->formatExpirationDate($consumable['ExpirationDate'])
+                    : '';
+
                 $this->reagents[] = [
                     'name' => $consumable['SerialNumber'],
-                    'expire_date' => isset($consumable['ExpirationDate'])
-                        ? $this->formatExpirationDate($consumable['ExpirationDate'])
-                        : '',
+                    'expire_date' => $expireDate,
                 ];
 
                 if ($type === 'DryCartridge') {
                     $this->flowcell = $consumable['SerialNumber'];
-                    if (isset($consumable['ExpirationDate'])) {
-                        $this->flowcellExpirationDate = $this->formatExpirationDate($consumable['ExpirationDate']);
+                    if ($expireDate !== '') {
+                        $this->flowcellExpirationDate = $expireDate;
                     }
                 }
             }
         }
     }
 
-    private function stripZeroPrefix(string $serial): string
+    protected function stripZeroPrefix(string $serial): string
     {
         $pos = strpos($serial, '-');
         if ($pos === false) {
             return $serial;
         }
 
-        $prefix = substr($serial, 0, $pos); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
+        $prefix = substr($serial, 0, $pos); // @phpstan-ignore theCodingMachineSafe.function (safe from PHP 8.0)
         if ($prefix !== '' && trim($prefix, '0') === '') {
-            return substr($serial, $pos + 1); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
+            return substr($serial, $pos + 1); // @phpstan-ignore theCodingMachineSafe.function (safe from PHP 8.0)
         }
 
         return $serial;
     }
 
-    private function formatExpirationDate(string $dateTime): string
+    protected function formatExpirationDate(string $dateTime): string
     {
-        $date = Carbon::parse($dateTime);
+        $formats = [DATE_ATOM, 'Y-m-d\TH:i:s'];
+
+        foreach ($formats as $format) {
+            try {
+                $date = Carbon::createFromFormat($format, $dateTime);
+                if ($date instanceof Carbon) {
+                    return $date->format('Y-m-d');
+                }
+            } catch (\Carbon\Exceptions\InvalidFormatException $e) {
+                continue;
+            }
+        }
 
-        return $date->format('Y-m-d');
+        throw new InterOpException("Failed to parse expiration date: {$dateTime}.");
     }
 }

From c6aef618cdabc9e67f573d455c926215564c89d9 Mon Sep 17 00:00:00 2001
From: Simon Bigelmayr <simon.bigelmayr@mll.com>
Date: Mon, 27 Apr 2026 12:35:03 +0200
Subject: [PATCH 13/25] fix(phpstan): use @phpstan-ignore-line for
 cross-version compatibility
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

@phpstan-ignore only works in PHPStan 2.x, while @phpstan-ignore-line
is recognized by both PHPStan 1.x and 2.x.

🤖 Generated with Claude Code
---
 src/InterOp/InterOpResult.php | 2 +-
 src/InterOp/RunParameters.php | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index cf12515..17ad131 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -57,7 +57,7 @@ public static function findDataReads(array $summary): array
                 continue;
             }
 
-            if (substr($level, -3) !== '(I)') { // @phpstan-ignore theCodingMachineSafe.function (safe from PHP 8.0)
+            if (substr($level, -3) !== '(I)') { // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
                 $dataReads[] = $level;
             }
         }
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index abc7694..e6f4b31 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -112,7 +112,7 @@ protected function parseMiSeqI100(array $params): void
         $this->controlSoftwareVersion = $params['SystemSuiteVersion'];
         $this->realTimeAnalysisVersion = null;
 
-        $dateString = substr($this->info, 0, 8); // @phpstan-ignore theCodingMachineSafe.function (safe from PHP 8.0)
+        $dateString = substr($this->info, 0, 8); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
         $date = Carbon::createFromFormat('!Ymd', $dateString);
         assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$this->info}.");
         $this->runDate = $date;
@@ -152,9 +152,9 @@ protected function stripZeroPrefix(string $serial): string
             return $serial;
         }
 
-        $prefix = substr($serial, 0, $pos); // @phpstan-ignore theCodingMachineSafe.function (safe from PHP 8.0)
+        $prefix = substr($serial, 0, $pos); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
         if ($prefix !== '' && trim($prefix, '0') === '') {
-            return substr($serial, $pos + 1); // @phpstan-ignore theCodingMachineSafe.function (safe from PHP 8.0)
+            return substr($serial, $pos + 1); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
         }
 
         return $serial;

From 2606058d954460542336c2323bb94574c4c109f2 Mon Sep 17 00:00:00 2001
From: Simon Bigelmayr <simon.bigelmayr@mll.com>
Date: Mon, 27 Apr 2026 12:51:52 +0200
Subject: [PATCH 14/25] fix: replace assert() with exceptions for runtime
 validation
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

assert() is compiled out in production (zend.assertions=-1), so
invalid external data would silently propagate as null/TypeError.
Also adds missing test for DeviationValue::average().

🤖 Generated with Claude Code
---
 src/InterOp/LaneResult.php           | 29 ++++++++++++++++++++--------
 src/InterOp/RunParameters.php        |  8 ++++++--
 tests/InterOp/DeviationValueTest.php | 11 +++++++++++
 3 files changed, 38 insertions(+), 10 deletions(-)

diff --git a/src/InterOp/LaneResult.php b/src/InterOp/LaneResult.php
index 8c2debf..5caec53 100644
--- a/src/InterOp/LaneResult.php
+++ b/src/InterOp/LaneResult.php
@@ -31,24 +31,37 @@ public function __construct(ClusterStatistic $clusterStatistic, SequencingQualit
     public static function fromInterOpRow(array $row): self
     {
         $density = DeviationValue::parse($row['Density']);
-        assert($density instanceof DeviationValue, "Expected parseable Density, got: {$row['Density']}.");
+        if (! $density instanceof DeviationValue) {
+            throw new InterOpException("Expected parseable Density, got: {$row['Density']}.");
+        }
 
         $clusterPassingFilter = DeviationValue::parse($row['Cluster PF']);
-        assert($clusterPassingFilter instanceof DeviationValue, "Expected parseable Cluster PF, got: {$row['Cluster PF']}.");
+        if (! $clusterPassingFilter instanceof DeviationValue) {
+            throw new InterOpException("Expected parseable Cluster PF, got: {$row['Cluster PF']}.");
+        }
 
         $aligned = DeviationValue::parse($row['Aligned']);
-        assert($aligned instanceof DeviationValue, "Expected parseable Aligned, got: {$row['Aligned']}.");
+        if (! $aligned instanceof DeviationValue) {
+            throw new InterOpException("Expected parseable Aligned, got: {$row['Aligned']}.");
+        }
 
         $error = DeviationValue::parse($row['Error']);
-        assert($error instanceof DeviationValue, "Expected parseable Error, got: {$row['Error']}.");
+        if (! $error instanceof DeviationValue) {
+            throw new InterOpException("Expected parseable Error, got: {$row['Error']}.");
+        }
 
         $intensityCycle = DeviationValue::parse($row['Intensity C1']);
-        assert($intensityCycle instanceof DeviationValue, "Expected parseable Intensity C1, got: {$row['Intensity C1']}.");
+        if (! $intensityCycle instanceof DeviationValue) {
+            throw new InterOpException("Expected parseable Intensity C1, got: {$row['Intensity C1']}.");
+        }
 
         $phasingParts = explode(' / ', $row['Legacy Phasing/Prephasing Rate']);
-        assert(count($phasingParts) === 2, "Expected 'phasing / prephasing' format, got: {$row['Legacy Phasing/Prephasing Rate']}.");
-        assert($phasingParts[0] !== 'nan', 'Unexpected nan phasing rate for data read.');
-        assert($phasingParts[1] !== 'nan', 'Unexpected nan prephasing rate for data read.');
+        if (count($phasingParts) !== 2) {
+            throw new InterOpException("Expected 'phasing / prephasing' format, got: {$row['Legacy Phasing/Prephasing Rate']}.");
+        }
+        if ($phasingParts[0] === 'nan' || $phasingParts[1] === 'nan') {
+            throw new InterOpException('Unexpected nan phasing rate for data read.');
+        }
 
         $clusterStatistic = new ClusterStatistic(
             $density,
diff --git a/src/InterOp/RunParameters.php b/src/InterOp/RunParameters.php
index e6f4b31..25b4b45 100644
--- a/src/InterOp/RunParameters.php
+++ b/src/InterOp/RunParameters.php
@@ -81,7 +81,9 @@ protected function parseMiSeq(array $params): void
 
         $runStartDate = str_pad(SafeCast::toString($params['RunStartDate']), 6, '0', STR_PAD_LEFT);
         $date = Carbon::createFromFormat('!ymd', $runStartDate);
-        assert($date instanceof Carbon, "Failed to parse MiSeq RunStartDate: {$runStartDate}.");
+        if (! $date instanceof Carbon) {
+            throw new InterOpException("Failed to parse MiSeq RunStartDate: {$runStartDate}.");
+        }
         $this->runDate = $date;
 
         $this->flowcell = $this->stripZeroPrefix($params['FlowcellRFIDTag']['SerialNumber']);
@@ -114,7 +116,9 @@ protected function parseMiSeqI100(array $params): void
 
         $dateString = substr($this->info, 0, 8); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
         $date = Carbon::createFromFormat('!Ymd', $dateString);
-        assert($date instanceof Carbon, "Failed to parse i100 run date from RunId: {$this->info}.");
+        if (! $date instanceof Carbon) {
+            throw new InterOpException("Failed to parse i100 run date from RunId: {$this->info}.");
+        }
         $this->runDate = $date;
 
         $consumables = $params['ConsumableInfo']['ConsumableInfo'];
diff --git a/tests/InterOp/DeviationValueTest.php b/tests/InterOp/DeviationValueTest.php
index 84da30f..5380788 100644
--- a/tests/InterOp/DeviationValueTest.php
+++ b/tests/InterOp/DeviationValueTest.php
@@ -25,6 +25,17 @@ public function testParse(string $input, ?float $expectedValue, ?float $expected
         self::assertSame($expectedDeviation, $result->deviation);
     }
 
+    public function testAverage(): void
+    {
+        $a = new DeviationValue(100.0, 10.0);
+        $b = new DeviationValue(200.0, 30.0);
+
+        $avg = DeviationValue::average($a, $b);
+
+        self::assertSame(150.0, $avg->value);
+        self::assertSame(20.0, $avg->deviation);
+    }
+
     /** @return iterable<string, array{input: string, expectedValue: float|null, expectedDeviation: float|null}> */
     public static function parseProvider(): iterable
     {

From cdb249d38bad7dcef77757682105bf1240ef1178 Mon Sep 17 00:00:00 2001
From: Simon Bigelmayr <simon.bigelmayr@mll.com>
Date: Mon, 27 Apr 2026 13:25:11 +0200
Subject: [PATCH 15/25] fix(phpstan): restore assert for preg_match offset
 access
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

PHPStan 2.x needs assert(isset()) to narrow preg_match capture
types, even when the match return value guarantees their existence.

🤖 Generated with Claude Code
---
 src/InterOp/DeviationValue.php | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/InterOp/DeviationValue.php b/src/InterOp/DeviationValue.php
index 91131d2..92630aa 100644
--- a/src/InterOp/DeviationValue.php
+++ b/src/InterOp/DeviationValue.php
@@ -28,6 +28,7 @@ public static function parse(string $raw): ?self
         if (preg_match('/^([\d.]+)\s*\+\/-\s*([\d.]+)$/', $raw, $matches) !== 1) {
             return null;
         }
+        assert(isset($matches[1], $matches[2]));
 
         return new self(
             SafeCast::toFloat($matches[1]),

From 5e7981db2e4ce970ea36da42ac3e0e0b2364aad9 Mon Sep 17 00:00:00 2001
From: Simon Bigelmayr <simon.bigelmayr@mll.com>
Date: Mon, 27 Apr 2026 13:27:42 +0200
Subject: [PATCH 16/25] fix: validate required row keys in
 LaneResult::fromInterOpRow()
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Missing or renamed keys would silently produce null and propagate
through SafeCast/DeviationValue. Validate all expected keys upfront.

🤖 Generated with Claude Code
---
 src/InterOp/LaneResult.php | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/InterOp/LaneResult.php b/src/InterOp/LaneResult.php
index 5caec53..a436f93 100644
--- a/src/InterOp/LaneResult.php
+++ b/src/InterOp/LaneResult.php
@@ -30,6 +30,12 @@ public function __construct(ClusterStatistic $clusterStatistic, SequencingQualit
      */
     public static function fromInterOpRow(array $row): self
     {
+        $requiredKeys = ['Density', 'Cluster PF', 'Aligned', 'Error', 'Intensity C1', 'Legacy Phasing/Prephasing Rate', 'Reads', 'Reads PF', '%>=Q30', 'Yield'];
+        $missingKeys = array_diff($requiredKeys, array_keys($row));
+        if ($missingKeys !== []) {
+            throw new InterOpException('Missing InterOp row keys: ' . implode(', ', $missingKeys) . '.');
+        }
+
         $density = DeviationValue::parse($row['Density']);
         if (! $density instanceof DeviationValue) {
             throw new InterOpException("Expected parseable Density, got: {$row['Density']}.");

From 8237496f3635f17ad55d10d5f432eb7f1afba46f Mon Sep 17 00:00:00 2001
From: Simon Bigelmayr <simon.bigelmayr@mll.com>
Date: Mon, 27 Apr 2026 13:35:36 +0200
Subject: [PATCH 17/25] refactor: extract MetaInfo payload type to class-level
 PHPDoc
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Moves the inline @var type annotation from the constructor to a
@phpstan-type on the class, improving readability.

🤖 Generated with Claude Code
---
 src/InterOp/MetaInfo.php | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/src/InterOp/MetaInfo.php b/src/InterOp/MetaInfo.php
index d866bf0..665c441 100644
--- a/src/InterOp/MetaInfo.php
+++ b/src/InterOp/MetaInfo.php
@@ -7,6 +7,14 @@
 /**
  * @phpstan-import-type MiSeqParams from RunParameters
  * @phpstan-import-type I100Params from RunParameters
+ * @phpstan-type MetaInfoPayload array{
+ *     runParameters: array{RunParameters: MiSeqParams|I100Params},
+ *     interop: array{
+ *         summary: array<int, array<string, string>>,
+ *         reads: array<string, array<int, array<string, string>>>,
+ *     },
+ *     uncPath: string,
+ * }
  */
 class MetaInfo
 {
@@ -18,16 +26,7 @@ class MetaInfo
 
     public function __construct(string $json)
     {
-        /**
-         * @var array{
-         *     runParameters: array{RunParameters: MiSeqParams|I100Params},
-         *     interop: array{
-         *         summary: array<int, array<string, string>>,
-         *         reads: array<string, array<int, array<string, string>>>,
-         *     },
-         *     uncPath: string,
-         * } $data
-         */
+        /** @var MetaInfoPayload $data */
         $data = json_decode($json, true);
 
         $this->runParameters = new RunParameters($data['runParameters']['RunParameters']);

From 20e8e391dac3fc58741ea58415f76f2f7c09ec4c Mon Sep 17 00:00:00 2001
From: simbig <26680884+simbig@users.noreply.github.com>
Date: Mon, 27 Apr 2026 11:36:09 +0000
Subject: [PATCH 18/25] Apply php-cs-fixer changes

---
 src/InterOp/MetaInfo.php | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/InterOp/MetaInfo.php b/src/InterOp/MetaInfo.php
index 665c441..c99452d 100644
--- a/src/InterOp/MetaInfo.php
+++ b/src/InterOp/MetaInfo.php
@@ -7,6 +7,7 @@
 /**
  * @phpstan-import-type MiSeqParams from RunParameters
  * @phpstan-import-type I100Params from RunParameters
+ *
  * @phpstan-type MetaInfoPayload array{
  *     runParameters: array{RunParameters: MiSeqParams|I100Params},
  *     interop: array{

From 0e640b7c6a67eb8e524af6a4ef108ae254d3e2ad Mon Sep 17 00:00:00 2001
From: Simon Bigelmayr <simon.bigelmayr@mll.com>
Date: Mon, 27 Apr 2026 13:37:47 +0200
Subject: [PATCH 19/25] fix(phpstan): use native preg_match for capture type
 narrowing
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Safe\preg_match prevents PHPStan 2.x from narrowing capture group
types, causing offsetAccess.notFound errors. Use native preg_match
with @phpstan-ignore-line for thecodingmachine rule compatibility.

🤖 Generated with Claude Code
---
 src/InterOp/DeviationValue.php | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/InterOp/DeviationValue.php b/src/InterOp/DeviationValue.php
index 92630aa..bf6ba73 100644
--- a/src/InterOp/DeviationValue.php
+++ b/src/InterOp/DeviationValue.php
@@ -4,8 +4,6 @@
 
 use MLL\Utils\SafeCast;
 
-use function Safe\preg_match;
-
 class DeviationValue
 {
     public float $value;
@@ -25,10 +23,9 @@ public function __construct(float $value, float $deviation)
      */
     public static function parse(string $raw): ?self
     {
-        if (preg_match('/^([\d.]+)\s*\+\/-\s*([\d.]+)$/', $raw, $matches) !== 1) {
+        if (preg_match('/^([\d.]+)\s*\+\/-\s*([\d.]+)$/', $raw, $matches) !== 1) { // @phpstan-ignore-line theCodingMachineSafe.function (native preg_match needed for PHPStan 2.x capture type narrowing)
             return null;
         }
-        assert(isset($matches[1], $matches[2]));
 
         return new self(
             SafeCast::toFloat($matches[1]),

From b7a1f2afa4a52a48df3a98ac62058ace7bc7fc93 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Wed, 29 Apr 2026 17:19:06 +0200
Subject: [PATCH 20/25] Prevent Single End Sequencing Results

---
 src/InterOp/InterOpResult.php | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index 17ad131..0d48654 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -50,6 +50,7 @@ public function __construct(array $summary, array $reads)
      */
     public static function findDataReads(array $summary): array
     {
+        // Summary count depends on indexing type (Sinlge or Dual) and sequencing type (Single-End or Paired-End). Possible reads are: Read 1, Read 2, Read 3, Non-indexed or Total
         $dataReads = [];
         foreach ($summary as $entry) {
             $level = $entry['Level'];
@@ -57,16 +58,20 @@ public static function findDataReads(array $summary): array
                 continue;
             }
 
+            // Identify index reads
             if (substr($level, -3) !== '(I)') { // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
                 $dataReads[] = $level;
             }
         }
 
         $count = count($dataReads);
-        if ($count < 2) {
-            throw new InterOpException("Expected at least 2 data reads, found {$count}.");
+        if ($count === 0 || $count > 2){
+            throw new InterOpException("Unlogic behaviour. Expect 2 data reads, found {$count}.");
+        }
+        if($count === 1){
+            throw new InterOpException("Single-End Sequencing results are not implemented.");
         }
 
-        return [$dataReads[0], $dataReads[$count - 1]];
+        return [$dataReads[0], $dataReads[1]];
     }
 }

From 2f59c68d3bc31fb733ea07660150f034b11a31ba Mon Sep 17 00:00:00 2001
From: dhaupt88 <133017448+dhaupt88@users.noreply.github.com>
Date: Wed, 29 Apr 2026 15:19:55 +0000
Subject: [PATCH 21/25] Apply php-cs-fixer changes

---
 src/InterOp/InterOpResult.php | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index 0d48654..7f9a6f4 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -65,11 +65,11 @@ public static function findDataReads(array $summary): array
         }
 
         $count = count($dataReads);
-        if ($count === 0 || $count > 2){
+        if ($count === 0 || $count > 2) {
             throw new InterOpException("Unlogic behaviour. Expect 2 data reads, found {$count}.");
         }
-        if($count === 1){
-            throw new InterOpException("Single-End Sequencing results are not implemented.");
+        if ($count === 1) {
+            throw new InterOpException('Single-End Sequencing results are not implemented.');
         }
 
         return [$dataReads[0], $dataReads[1]];

From 09be5e7a8ce39dfc706304841d1bb19406f0fe37 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Wed, 29 Apr 2026 17:39:23 +0200
Subject: [PATCH 22/25] Add assertions

---
 src/InterOp/ClusterStatistic.php    | 10 +++---
 src/InterOp/LaneResult.php          |  4 +--
 tests/InterOp/InterOpResultTest.php | 55 +++++++++++++++++++++++++++++
 tests/InterOp/MetaInfoTest.php      |  7 ++--
 tests/InterOp/RunParametersTest.php | 18 ++++++++++
 5 files changed, 85 insertions(+), 9 deletions(-)
 create mode 100644 tests/InterOp/RunParametersTest.php

diff --git a/src/InterOp/ClusterStatistic.php b/src/InterOp/ClusterStatistic.php
index 06b196e..a48b434 100644
--- a/src/InterOp/ClusterStatistic.php
+++ b/src/InterOp/ClusterStatistic.php
@@ -8,15 +8,15 @@ class ClusterStatistic
 
     public DeviationValue $clusterPassingFilter;
 
-    public float $clusterCount;
+    public float $clusterCountMillions;
 
-    public float $clusterCountPassingFilter;
+    public float $clusterCountPassingFilterMillions;
 
-    public function __construct(DeviationValue $density, DeviationValue $clusterPassingFilter, float $clusterCount, float $clusterCountPassingFilter)
+    public function __construct(DeviationValue $density, DeviationValue $clusterPassingFilter, float $clusterCountMillions, float $clusterCountPassingFilterMillions)
     {
         $this->density = $density;
         $this->clusterPassingFilter = $clusterPassingFilter;
-        $this->clusterCount = $clusterCount;
-        $this->clusterCountPassingFilter = $clusterCountPassingFilter;
+        $this->clusterCountMillions = $clusterCountMillions;
+        $this->clusterCountPassingFilterMillions = $clusterCountPassingFilterMillions;
     }
 }
diff --git a/src/InterOp/LaneResult.php b/src/InterOp/LaneResult.php
index a436f93..e37f16e 100644
--- a/src/InterOp/LaneResult.php
+++ b/src/InterOp/LaneResult.php
@@ -97,8 +97,8 @@ public static function aggregate(self $a, self $b): self
         $clusterStatistic = new ClusterStatistic(
             DeviationValue::average($a->clusterStatistic->density, $b->clusterStatistic->density),
             DeviationValue::average($a->clusterStatistic->clusterPassingFilter, $b->clusterStatistic->clusterPassingFilter),
-            $a->clusterStatistic->clusterCount + $b->clusterStatistic->clusterCount,
-            $a->clusterStatistic->clusterCountPassingFilter + $b->clusterStatistic->clusterCountPassingFilter
+            $a->clusterStatistic->clusterCountMillions + $b->clusterStatistic->clusterCountMillions,
+            $a->clusterStatistic->clusterCountPassingFilterMillions + $b->clusterStatistic->clusterCountPassingFilterMillions
         );
 
         $sequencingQualityControl = new SequencingQualityControl(
diff --git a/tests/InterOp/InterOpResultTest.php b/tests/InterOp/InterOpResultTest.php
index f917557..55fb700 100644
--- a/tests/InterOp/InterOpResultTest.php
+++ b/tests/InterOp/InterOpResultTest.php
@@ -2,6 +2,7 @@
 
 namespace MLL\Utils\Tests\InterOp;
 
+use MLL\Utils\InterOp\InterOpException;
 use MLL\Utils\InterOp\InterOpResult;
 use PHPUnit\Framework\Attributes\DataProvider;
 use PHPUnit\Framework\TestCase;
@@ -22,6 +23,60 @@ public function testFindDataReads(string $description, array $summary, string $e
         self::assertSame($expectedLast, $last, "{$description}: last data read");
     }
 
+    public function testThrowsOnNoDataReads(): void
+    {
+        $this->expectException(InterOpException::class);
+
+        InterOpResult::findDataReads([
+            ['Level' => 'Read 1 (I)'],
+            ['Level' => 'Read 2 (I)'],
+            ['Level' => 'Non-indexed'],
+            ['Level' => 'Total'],
+        ]);
+    }
+
+    public function testThrowsOnSingleDataRead(): void
+    {
+        $this->expectException(InterOpException::class);
+
+        InterOpResult::findDataReads([
+            ['Level' => 'Read 1'],
+            ['Level' => 'Read 2 (I)'],
+            ['Level' => 'Non-indexed'],
+            ['Level' => 'Total'],
+        ]);
+    }
+
+    public function testThrowsOnMissingReadData(): void
+    {
+        $summary = [
+            ['Level' => 'Read 1'],
+            ['Level' => 'Read 2 (I)'],
+            ['Level' => 'Read 3'],
+            ['Level' => 'Non-indexed'],
+            ['Level' => 'Total'],
+        ];
+
+        $this->expectException(InterOpException::class);
+
+        new InterOpResult($summary, []);
+    }
+
+    public function testThrowsOnEmptyReadRows(): void
+    {
+        $summary = [
+            ['Level' => 'Read 1'],
+            ['Level' => 'Read 2 (I)'],
+            ['Level' => 'Read 3'],
+            ['Level' => 'Non-indexed'],
+            ['Level' => 'Total'],
+        ];
+
+        $this->expectException(InterOpException::class);
+
+        new InterOpResult($summary, ['Read 1' => [], 'Read 3' => []]);
+    }
+
     /** @return iterable<string, array{description: string, summary: array<int, array<string, string>>, expectedFirst: string, expectedLast: string}> */
     public static function dataReadDetectionProvider(): iterable
     {
diff --git a/tests/InterOp/MetaInfoTest.php b/tests/InterOp/MetaInfoTest.php
index db9a3ab..5aa192e 100644
--- a/tests/InterOp/MetaInfoTest.php
+++ b/tests/InterOp/MetaInfoTest.php
@@ -31,8 +31,8 @@ public function testParseMiSeq(): void
         self::assertSame(851.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->value);
         self::assertSame(32.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->deviation);
         self::assertSame(96.54, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterPassingFilter->value);
-        self::assertSame(21.22, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCount);
-        self::assertSame(20.48, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCountPassingFilter);
+        self::assertSame(21.22, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCountMillions);
+        self::assertSame(20.48, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCountPassingFilterMillions);
 
         self::assertSame(88.2, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->q30);
         self::assertSame(0.085, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->phasing);
@@ -74,7 +74,10 @@ public function testParseMiSeqI100(): void
         self::assertSame('2026-10-17', $metaInfo->runParameters->reagents[1]['expire_date']);
 
         self::assertSame(1000.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->value);
+        self::assertSame(0.0, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->density->deviation);
         self::assertSame(62.27, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterPassingFilter->value);
+        self::assertSame(7.91, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCountMillions);
+        self::assertSame(4.92, $metaInfo->interOpResult->resultsForRead1->clusterStatistic->clusterCountPassingFilterMillions);
         self::assertSame(95.35, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->q30);
         self::assertSame(0.075, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->phasing);
         self::assertSame(0.042, $metaInfo->interOpResult->resultsForRead1->sequencingQualityControl->prephasing);
diff --git a/tests/InterOp/RunParametersTest.php b/tests/InterOp/RunParametersTest.php
new file mode 100644
index 0000000..139e906
--- /dev/null
+++ b/tests/InterOp/RunParametersTest.php
@@ -0,0 +1,18 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\InterOp;
+
+use MLL\Utils\InterOp\InterOpException;
+use MLL\Utils\InterOp\RunParameters;
+use PHPUnit\Framework\TestCase;
+
+final class RunParametersTest extends TestCase
+{
+    public function testThrowsOnUnknownDeviceType(): void
+    {
+        $this->expectException(InterOpException::class);
+
+        // @phpstan-ignore argument.type (intentionally invalid input for error path test)
+        new RunParameters(['UnknownKey' => 'value']);
+    }
+}

From b52b71a06b3dbf4c11e860169f2c850378fff4e3 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Thu, 30 Apr 2026 09:07:54 +0200
Subject: [PATCH 23/25] Use non-index result as well

---
 src/InterOp/InterOpResult.php  | 20 +++++++++++++++++++-
 src/InterOp/RunResult.php      | 21 +++++++++++++++++++--
 tests/InterOp/MetaInfoTest.php |  3 ++-
 3 files changed, 40 insertions(+), 4 deletions(-)

diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index 7f9a6f4..7426258 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -28,10 +28,12 @@ public function __construct(array $summary, array $reads)
             throw new InterOpException("Reads data missing or empty for: {$lastDataRead}.");
         }
 
+        $nonIndexedRow = self::findNonIndexedRow($summary);
+
         // First row per read key is the Surface "-" aggregate across all tiles
         $this->resultsForRead1 = LaneResult::fromInterOpRow($read1Rows[0]);
         $this->resultsForRead2 = LaneResult::fromInterOpRow($read2Rows[0]);
-        $this->resultsForRun = RunResult::fromLaneResults($this->resultsForRead1, $this->resultsForRead2);
+        $this->resultsForRun = RunResult::fromLaneResults($this->resultsForRead1, $this->resultsForRead2, $nonIndexedRow);
     }
 
     /**
@@ -74,4 +76,20 @@ public static function findDataReads(array $summary): array
 
         return [$dataReads[0], $dataReads[1]];
     }
+
+    /**
+     * @param array<int, array<string, string>> $summary
+     *
+     * @return array<string, string>
+     */
+    public static function findNonIndexedRow(array $summary): array
+    {
+        foreach ($summary as $entry) {
+            if ($entry['Level'] === 'Non-indexed') {
+                return $entry;
+            }
+        }
+
+        throw new InterOpException('No "Non-indexed" summary row found.');
+    }
 }
diff --git a/src/InterOp/RunResult.php b/src/InterOp/RunResult.php
index f8e4d69..840f224 100644
--- a/src/InterOp/RunResult.php
+++ b/src/InterOp/RunResult.php
@@ -2,6 +2,8 @@
 
 namespace MLL\Utils\InterOp;
 
+use MLL\Utils\SafeCast;
+
 class RunResult
 {
     public ClusterStatistic $clusterStatistic;
@@ -14,10 +16,25 @@ public function __construct(ClusterStatistic $clusterStatistic, SequencingQualit
         $this->sequencingQualityControl = $sequencingQualityControl;
     }
 
-    public static function fromLaneResults(LaneResult $read1, LaneResult $read2): self
+    /** @param array<string, string> $nonIndexedRow */
+    public static function fromLaneResults(LaneResult $read1, LaneResult $read2, array $nonIndexedRow): self
     {
         $aggregated = LaneResult::aggregate($read1, $read2);
 
-        return new self($aggregated->clusterStatistic, $aggregated->sequencingQualityControl);
+        $q30 = SafeCast::toFloat($nonIndexedRow['%>=Q30']);
+
+        $alignedValue = SafeCast::toFloat($nonIndexedRow['Aligned']);
+        $alignedDeviation = ($read1->sequencingQualityControl->aligned->deviation + $read2->sequencingQualityControl->aligned->deviation) / 2;
+        $aligned = new DeviationValue($alignedValue, $alignedDeviation);
+
+        $sequencingQualityControl = new SequencingQualityControl(
+            $q30,
+            $aggregated->sequencingQualityControl->phasing,
+            $aggregated->sequencingQualityControl->prephasing,
+            $aligned,
+            $aggregated->sequencingQualityControl->error
+        );
+
+        return new self($aggregated->clusterStatistic, $sequencingQualityControl);
     }
 }
diff --git a/tests/InterOp/MetaInfoTest.php b/tests/InterOp/MetaInfoTest.php
index 5aa192e..4b0074d 100644
--- a/tests/InterOp/MetaInfoTest.php
+++ b/tests/InterOp/MetaInfoTest.php
@@ -48,7 +48,8 @@ public function testParseMiSeq(): void
         self::assertSame(6140000, $metaInfo->interOpResult->resultsForRead2->yield);
 
         $runQC = $metaInfo->interOpResult->resultsForRun->sequencingQualityControl;
-        self::assertEqualsWithDelta(83.195, $runQC->q30, 0.001);
+        self::assertSame(83.2, $runQC->q30);
+        self::assertSame(6.11, $runQC->aligned->value);
         self::assertEqualsWithDelta(0.065, $runQC->phasing, 0.001);
 
         self::assertSame('example-server/miseq_active\\230421_M02074_0859_000000000-KT6CY\\meta-info.json', $metaInfo->uncPath);

From bf6416a1aaeb172e74c99ffb0829338afbd1485a Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Thu, 30 Apr 2026 15:00:25 +0200
Subject: [PATCH 24/25] Use non-index result as well

---
 src/InterOp/InterOpResult.php       | 20 ++++++++++----------
 tests/InterOp/InterOpResultTest.php |  6 +++---
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/InterOp/InterOpResult.php b/src/InterOp/InterOpResult.php
index 7426258..32109ea 100644
--- a/src/InterOp/InterOpResult.php
+++ b/src/InterOp/InterOpResult.php
@@ -16,16 +16,16 @@ class InterOpResult
      */
     public function __construct(array $summary, array $reads)
     {
-        [$firstDataRead, $lastDataRead] = self::findDataReads($summary);
+        [$dataRead1Tag, $dataRead2Tag] = self::findDataReadTags($summary);
 
-        $read1Rows = $reads[$firstDataRead] ?? null;
+        $read1Rows = $reads[$dataRead1Tag] ?? null;
         if ($read1Rows === null || $read1Rows === []) {
-            throw new InterOpException("Reads data missing or empty for: {$firstDataRead}.");
+            throw new InterOpException("Reads data missing or empty for: {$dataRead1Tag}.");
         }
 
-        $read2Rows = $reads[$lastDataRead] ?? null;
+        $read2Rows = $reads[$dataRead2Tag] ?? null;
         if ($read2Rows === null || $read2Rows === []) {
-            throw new InterOpException("Reads data missing or empty for: {$lastDataRead}.");
+            throw new InterOpException("Reads data missing or empty for: {$dataRead2Tag}.");
         }
 
         $nonIndexedRow = self::findNonIndexedRow($summary);
@@ -50,10 +50,10 @@ public function __construct(array $summary, array $reads)
      *
      * @return array{0: string, 1: string}
      */
-    public static function findDataReads(array $summary): array
+    public static function findDataReadTags(array $summary): array
     {
         // Summary count depends on indexing type (Sinlge or Dual) and sequencing type (Single-End or Paired-End). Possible reads are: Read 1, Read 2, Read 3, Non-indexed or Total
-        $dataReads = [];
+        $dataReadTags = [];
         foreach ($summary as $entry) {
             $level = $entry['Level'];
             if ($level === 'Non-indexed' || $level === 'Total') {
@@ -62,11 +62,11 @@ public static function findDataReads(array $summary): array
 
             // Identify index reads
             if (substr($level, -3) !== '(I)') { // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
-                $dataReads[] = $level;
+                $dataReadTags[] = $level;
             }
         }
 
-        $count = count($dataReads);
+        $count = count($dataReadTags);
         if ($count === 0 || $count > 2) {
             throw new InterOpException("Unlogic behaviour. Expect 2 data reads, found {$count}.");
         }
@@ -74,7 +74,7 @@ public static function findDataReads(array $summary): array
             throw new InterOpException('Single-End Sequencing results are not implemented.');
         }
 
-        return [$dataReads[0], $dataReads[1]];
+        return [$dataReadTags[0], $dataReadTags[1]];
     }
 
     /**
diff --git a/tests/InterOp/InterOpResultTest.php b/tests/InterOp/InterOpResultTest.php
index 55fb700..5a58229 100644
--- a/tests/InterOp/InterOpResultTest.php
+++ b/tests/InterOp/InterOpResultTest.php
@@ -17,7 +17,7 @@ final class InterOpResultTest extends TestCase
     #[DataProvider('dataReadDetectionProvider')]
     public function testFindDataReads(string $description, array $summary, string $expectedFirst, string $expectedLast): void
     {
-        [$first, $last] = InterOpResult::findDataReads($summary);
+        [$first, $last] = InterOpResult::findDataReadTags($summary);
 
         self::assertSame($expectedFirst, $first, "{$description}: first data read");
         self::assertSame($expectedLast, $last, "{$description}: last data read");
@@ -27,7 +27,7 @@ public function testThrowsOnNoDataReads(): void
     {
         $this->expectException(InterOpException::class);
 
-        InterOpResult::findDataReads([
+        InterOpResult::findDataReadTags([
             ['Level' => 'Read 1 (I)'],
             ['Level' => 'Read 2 (I)'],
             ['Level' => 'Non-indexed'],
@@ -39,7 +39,7 @@ public function testThrowsOnSingleDataRead(): void
     {
         $this->expectException(InterOpException::class);
 
-        InterOpResult::findDataReads([
+        InterOpResult::findDataReadTags([
             ['Level' => 'Read 1'],
             ['Level' => 'Read 2 (I)'],
             ['Level' => 'Non-indexed'],

From 2b977b76e4d34bd1a7cd9bd058af31a5c34745d2 Mon Sep 17 00:00:00 2001
From: Dennis Haupt <dennis.haupt@mll.com>
Date: Thu, 30 Apr 2026 15:11:04 +0200
Subject: [PATCH 25/25] Fix stan

---
 phpstan/php-below-8.1.neon | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/phpstan/php-below-8.1.neon b/phpstan/php-below-8.1.neon
index a2f3659..9a45de4 100644
--- a/phpstan/php-below-8.1.neon
+++ b/phpstan/php-below-8.1.neon
@@ -34,3 +34,5 @@ parameters:
     # Existing code with @phpstan-ignore that older versions don't understand
     - message: '#Cannot access property \$name on SimpleXMLElement\|null\.#'
       path: ../src/LightcyclerExportSheet/LightcyclerXmlParser.php
+    - message: '#array\{UnknownKey: .* given\.#'
+      path: ../tests/InterOp/RunParametersTest.php