Add back REF/ALT to csv output in addition to resolved GT fields#83
Add back REF/ALT to csv output in addition to resolved GT fields#83nalinigans merged 1 commit intodevelopfrom
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| // Process REF, ALT and GT first. | ||
| process_str_field("REF", calls, dims, sizes); | ||
| process_str_field("ALT", calls, dims, sizes); | ||
| process_str_field("GT", calls, dims, sizes); |
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Naive question: can you tell me why we process REF, ALT, GT first instead of in the loop?
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They could be in any order based on how GenomicsDB processes them. We could let the loop handle it, but sometimes, the order is ALT,REF,..,GT. I just thought it nicer to have REF before ALT, guess it does not matter for GT as much.. But, I can process them in the loop if that is OK too. Let me know.
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Yeah, can't decide. My initial concern was that this bit of code gets invoked for each variant so trying to minimize any extraneous code. But that's probably micro-optimization...thoughts?
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This bit of code is not invoked per variant call, it happens only once per query - see. The calls themselves are already populated as m_string_fields in the dictionary backed by std::map<std::string, std::vector<PyObject *>> m_string_fields as part of the code here. That said, I could probably order them at initialization.
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Ah - thanks for that clarification, I misread this as being part of process somehow. I think this is good to merge the way it is if you want.
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