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Bugfix absent phase information in annotation file

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

When creating a pangenome with some virus genomes, I noticed that the phase of CDS features is set to -1 if absent in the annotation. However, we use the phase information as index for translating coding sequences. Therefore, assume phase is 0 if not specified in annotation file.

Edited by Workum, Dirk-Jan van

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