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fischerlfischerl
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Illumina sample sheet v1 pairing (#23)
* feature: Add Support Illumina NovaSeq Sample Sheets
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‎CHANGELOG.md

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## Unreleased
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## v2.1.0
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### Added
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- Support creating Illumina Sample Sheets (V1) for NovaSeq
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## v2.0.0
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### Changed

‎src/IlluminaSampleSheet/SampleSheet.php renamed to ‎src/IlluminaSampleSheet/BaseSampleSheet.php

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namespace MLL\Utils\IlluminaSampleSheet;
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abstract class SampleSheet
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abstract class BaseSampleSheet
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{
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/** @var array<Section> */
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protected array $sections = [];

‎src/IlluminaSampleSheet/V1/DataSection.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\IlluminaSampleSheet\V1;
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use Illuminate\Support\Collection;
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use MLL\Utils\IlluminaSampleSheet\IlluminaSampleSheetException;
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use MLL\Utils\IlluminaSampleSheet\Section;
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/** @template TRow of Row */
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class DataSection implements Section
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{
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/** @var Collection<int, TRow> */
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public Collection $rows;
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/**
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* @param class-string<TRow> $rowClass
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*
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* @phpstan-ignore-next-line As of now, $rowClass is only used to enforce generic type instantiation.
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*/
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public function __construct(string $rowClass)
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{
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$this->rows = new Collection([]);
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}
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/** @param TRow $row */
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public function addRow(Row $row): void
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{
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$this->rows->add($row);
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}
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public function validate(): void
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{
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$this->validateDuplicatedSampleIDs();
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}
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public function convertSectionToString(): string
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{
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$this->validate();
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if ($this->rows->isEmpty()) {
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throw new IlluminaSampleSheetException('Data section must contain at least one row.');
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}
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/** @var Row $firstRow */
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$firstRow = $this->rows->first();
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$rowsData = $this->rows
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->map(fn (Row $row): string => $row->toString())
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->implode("\n");
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return "[Data]\n{$firstRow->headerLine()}\n{$rowsData}\n";
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}
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protected function validateDuplicatedSampleIDs(): void
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{
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$groups = $this->rows
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->groupBy(fn (Row $row) => $row->sampleID);
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$duplicates = $groups
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->filter(fn ($group) => count($group) > 1)
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->keys();
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$duplicateIDsAsString = $duplicates->implode(', ');
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if ($duplicates->isNotEmpty()) {
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throw new IlluminaSampleSheetException("Sample_ID values must be distinct. Duplicated SampleIDs: {$duplicateIDsAsString}");
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}
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}
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}

‎src/IlluminaSampleSheet/V1/DualIndex.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\IlluminaSampleSheet\V1;
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class DualIndex extends Index
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{
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public string $i7IndexID;
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public string $index;
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public string $i5IndexID;
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public string $index2;
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public function __construct(string $i7IndexID, string $index, string $i5IndexID, string $index2)
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{
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$this->i7IndexID = $i7IndexID;
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$this->index = $index;
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$this->i5IndexID = $i5IndexID;
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$this->index2 = $index2;
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$this->validate();
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}
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public function validate(): void
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{
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$this->validateIndex($this->index);
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$this->validateIndex($this->index2);
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}
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}

‎src/IlluminaSampleSheet/V1/HeaderSection.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\IlluminaSampleSheet\V1;
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use MLL\Utils\IlluminaSampleSheet\Section;
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class HeaderSection implements Section
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{
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public ?string $iemFileVersion;
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public ?string $experimentName;
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public ?string $investigatorName;
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public string $date;
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public string $workflow;
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public string $application;
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public string $assay;
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public string $description;
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public string $chemistry;
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public function __construct(
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string $iemFileVersion,
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string $investigatorName,
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string $experimentName,
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string $date,
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string $workflow,
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string $application,
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string $assay,
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string $description,
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string $chemistry
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) {
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$this->chemistry = $chemistry;
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$this->description = $description;
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$this->assay = $assay;
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$this->application = $application;
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$this->workflow = $workflow;
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$this->date = $date;
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$this->investigatorName = $investigatorName;
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$this->experimentName = $experimentName;
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$this->iemFileVersion = $iemFileVersion;
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}
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public function convertSectionToString(): string
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{
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$headerLines = [
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'[Header]',
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"IEMFileVersion,{$this->iemFileVersion}",
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"Investigator Name,{$this->investigatorName}",
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"Experiment Name,{$this->experimentName}",
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"Date,{$this->date}",
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"Workflow,{$this->workflow}",
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"Application,{$this->application}",
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"Assay,{$this->assay}",
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"Description,{$this->description}",
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"Chemistry,{$this->chemistry}",
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];
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return implode("\n", $headerLines);
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}
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}

‎src/IlluminaSampleSheet/V1/Index.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\IlluminaSampleSheet\V1;
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use MLL\Utils\IlluminaSampleSheet\IlluminaSampleSheetException;
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use function Safe\preg_match;
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abstract class Index
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{
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abstract public function validate(): void;
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protected function validateIndex(string $index): void
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{
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if ($index === '') {
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throw new IlluminaSampleSheetException('Index must not be an empty string.');
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}
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if (! (bool) preg_match('/^[ATCGN]+$/', $index)) {
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throw new IlluminaSampleSheetException("Index '{$index}' contains invalid characters. Only A, T, C, G, N are allowed.");
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}
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}
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}

‎src/IlluminaSampleSheet/V1/ReadsSection.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\IlluminaSampleSheet\V1;
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use MLL\Utils\IlluminaSampleSheet\Section;
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class ReadsSection implements Section
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{
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private int $read1Cycles;
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private int $read2Cycles;
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public function __construct(int $read1Cycles, int $read2Cycles)
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{
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$this->read1Cycles = $read1Cycles;
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$this->read2Cycles = $read2Cycles;
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}
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public function convertSectionToString(): string
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{
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return "[Reads]\n" . $this->read1Cycles . "\n" . $this->read2Cycles;
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}
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}

‎src/IlluminaSampleSheet/V1/Row.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\IlluminaSampleSheet\V1;
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abstract class Row
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{
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public string $sampleID;
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abstract public function toString(): string;
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abstract public function headerLine(): string;
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}

‎src/IlluminaSampleSheet/V1/RowForDualIndexWithLane.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\IlluminaSampleSheet\V1;
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class RowForDualIndexWithLane extends Row
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{
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public DualIndex $dualIndex;
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public int $lane;
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public string $sampleName;
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public string $samplePlate;
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public string $sampleWell;
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public string $sampleProject;
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public string $description;
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public function __construct(DualIndex $dualIndex, int $lane, string $sampleID, string $sampleName, string $samplePlate, string $sampleWell, string $sampleProject, string $description)
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{
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$this->dualIndex = $dualIndex;
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$this->lane = $lane;
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$this->sampleID = $sampleID;
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$this->sampleName = $sampleName;
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$this->samplePlate = $samplePlate;
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$this->sampleWell = $sampleWell;
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$this->sampleProject = $sampleProject;
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$this->description = $description;
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}
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public function toString(): string
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{
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return implode(',', [
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$this->lane,
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$this->sampleID,
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$this->sampleName,
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$this->samplePlate,
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$this->sampleWell,
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$this->dualIndex->i7IndexID,
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$this->dualIndex->index,
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$this->dualIndex->i5IndexID,
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$this->dualIndex->index2,
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$this->sampleProject,
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$this->description,
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]);
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}
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public function headerLine(): string
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{
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return 'Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,Index,I5_Index_ID,Index2,Sample_Project,Description';
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}
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}

‎src/IlluminaSampleSheet/V1/RowForDualIndexWithoutLane.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\IlluminaSampleSheet\V1;
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class RowForDualIndexWithoutLane extends Row
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{
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public DualIndex $dualIndex;
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public string $sampleName;
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public string $samplePlate;
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public string $sampleWell;
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public string $sampleProject;
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public string $description;
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public function __construct(DualIndex $dualIndex, string $sampleID, string $sampleName, string $samplePlate, string $sampleWell, string $sampleProject, string $description)
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{
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$this->dualIndex = $dualIndex;
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$this->sampleID = $sampleID;
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$this->sampleName = $sampleName;
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$this->samplePlate = $samplePlate;
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$this->sampleWell = $sampleWell;
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$this->sampleProject = $sampleProject;
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$this->description = $description;
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}
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public function toString(): string
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{
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return implode(',', [
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$this->sampleID,
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$this->sampleName,
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$this->samplePlate,
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$this->sampleWell,
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$this->dualIndex->i7IndexID,
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$this->dualIndex->index,
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$this->dualIndex->i5IndexID,
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$this->dualIndex->index2,
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$this->sampleProject,
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$this->description,
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]);
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}
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public function headerLine(): string
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{
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return 'Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,Index,I5_Index_ID,Index2,Sample_Project,Description';
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}
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}

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