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Fix phase information of CDS nodes for translation of mRNA to protein

Workum, Dirk-Jan van requested to merge fix_phase_in_translating_mrna into master

We identified an issue with partial genes in the gene annotation, where PanTools seemed to use the wrong phase for translating CDS sequences to protein. In particular, this issue was identified with partial genes. However, PanTools should be able to create the correct translation for all these cases.

I still marked this as a draft, because I am not yet sure which of the two following strategies will be the simplest to implement:

  1. For the first (forward strand) or last (reverse strand), use the phase information for translation
  2. Use BioJava or another library for translation
Edited by Workum, Dirk-Jan van

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