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During assembly of hits when extracting a miscellaneous DNA reference target, the delta in identity percentage between two hits to be considered compatible has been reduced from 5% to 3.33%, initial test indicate slight improvement in recovery.
In some edge cases, when translating a CDS reference target set, the same nucleotide sequence can produce perfectly translated protein in more than a single reading frame, we give now priority to positive reading frames in case of a tie.
Latest pandas versions introduced breaking changes, we provide a fix.
When creating a new miscellaneous DNA reference from clustering, each target sequence in a reference locus can have different strands. We add a method to uniformize the strand per reference locus.
Added an option to the align step to --only_collect the extracted markers and exit afterwards (requested by Diego Morales)