Improvements to update with library #88
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dkhofer
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Looks good. A note for a future PR involving update-with-library (for example implementing chromosome_index to signify wether or not the original reference is included): could we also look at what the same functionality would look like if it didn't rely on a blockgroup at all, but as an "import" command? |
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This PR brings "update with library" in line with "update with fasta" for working with samples. With these changes, "update with library" takes a required --new-sample flag, creates the new sample, and adds the combinatorial library parts to the specified region (block group) of the new sample.
This also fixes a small problem with error reporting. If no block group is found with the specified region name, gen now errors with eg "No region found with name: PXB_PRIM2"
There's some other minor refactoring in this change, nothing too significant.