GeezerVison is showing github.com — Fix reverse complement calculation in CDSSequence.getCodingSequence (#1016) by nayanhasnolyf · Pull Request #1160 · biojava/biojava
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Fixes #1016
CDSSequence.getCodingSequence() was calling getSequenceAsString(getBioBegin(), getBioEnd(), getStrand()), which already returns the reverse complement for Strand.NEGATIVE via AbstractLocation.reverseSequence(). After that, getCodingSequence() had a second if (getStrand() == Strand.NEGATIVE) block that complemented the sequence again, cancelling out the complement and leaving the sequence only reversed.
Removed the redundant second complement block in CDSSequence.java and enabled the existing @Disabled test TranscriptSequenceTest.getCDNASeqNegativeStrand().
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