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Given a transcript sequence derived from a GeneSequence defined on reverse strand of a chromosomal sequence, the method getCodingSequence doesn't return the reverse complement, but just the reverse.
This seems to be due to the complement being made twice:
Given a transcript sequence derived from a GeneSequence defined on reverse strand of a chromosomal sequence, the method getCodingSequence doesn't return the reverse complement, but just the reverse.
This seems to be due to the complement being made twice:
in CDSSequence# getCodingSequence()
generates the reverse complement, but subsequent code makes a complementary sequence again, so the end result is simply a reversed sequence.
A simple fix might be just to remove this second complementation, but possibly it might be needed in some circumstances.
The bug is exposed by test TranscriptSequenceTest#getCDNASeqNegativeStrand()
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