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When running a larger simulated experiment with the new barcodes feature, I noticed two issues.
First, I had introduced a bug in how the strategies were turned on, so they were actually never turned on. And second, the barcode information was not output to the resulting fasta files, which limited the analysis of the results.
The two commits here should address these issues. The plan is to keep this pull request small which just these two commits, and then create other ones when I have implemented unit tests and barcodes in the live version.