feat: Implement logic for Chromosome.php, GenomicPosition.php and Gen…#76
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KingKong1213 wants to merge 9 commits intomasterfrom
Open
feat: Implement logic for Chromosome.php, GenomicPosition.php and Gen…#76KingKong1213 wants to merge 9 commits intomasterfrom
KingKong1213 wants to merge 9 commits intomasterfrom
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simbig
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Mar 3, 2026
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Gutes Fundament — die Value Objects sind sauber aufgebaut. Ein paar fachliche Punkte die ich vor dem Merge klären würde.
| && ( | ||
| $this->positionIsBetweenStartAndEnd($genomicRegion->start) | ||
| || $this->positionIsBetweenStartAndEnd($genomicRegion->end) | ||
| ); |
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Bug: Falsch bei vollständiger Überlappung
Wenn Region B die Region A komplett umschließt (z.B. A=chr11:20-30, B=chr11:10-40), liefert die Methode fälschlich false, weil weder B.start noch B.end innerhalb von A liegt.
Fix — die kanonische Intervall-Formel:
return $this->chromosome->equals($other->chromosome)
&& $this->start <= $other->end
&& $other->start <= $this->end;
src/Chromosome.php
Outdated
| ? new ReferenzGenome(ReferenzGenome::HG_19) | ||
| : new ReferenzGenome(ReferenzGenome::GRCH_37); | ||
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| $this->value = $matches[2]; |
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Case und M/MT normalisieren
- Die Regex ist case-insensitive, aber der gespeicherte Wert behält die Original-Schreibweise →
chrxundchrXwären bei Vergleichen ungleich. Fix:strtoupper($matches[2]) MundMTbezeichnen beide das Mitochondrien-Chromosom, werden aber als unterschiedliche Werte gespeichert.chrMTist zudem kein gültiger UCSC-Bezeichner (korrekt:chrM). Fix:MT→Mnormalisieren.
simbig
reviewed
Mar 3, 2026
src/GenomicRegion.php
Outdated
| return $position >= $this->start && $position <= $this->end; | ||
| } | ||
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| public function toString(?ReferenzGenome $referenceGenome = null): string |
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to NamingConvention mit UCSC/ENSEMBL. also es geht ja drum mittels welcher namingConvention es serialisiert werden soll, oder?
Fix example
…WithGenomicRegion and isCoveredByGenomicRegion
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GenomicRegion.php
Changes
Implement logic for Chromosome.php, GenomicPosition.php and GenomicRegion.php
Breaking changes