✨ scrape descriptions on encode #35
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dmiller15
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📝 fix borrows 🐛 fix quote injection
🐛 public func for default checks
dmiller15
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@dmiller15 , this looks good to me. Ready from your end? |
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Just tested it, and it's still working as intended. |
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thank you! |
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@dmiller15 , this fails tests/big.sh. Can you fix that? |
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Sure I'll take a look |
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Ok didn't notice that we'd added more tests, and the test logic is no longer true. I'll update that batch of tests and have a PR up today. |
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Followup work to #34.
I tried to tackle the task of INFO field description scraping requested in #33. Found rust-htslib pretty ill-equipped for the task, but I'm way too much of a rust/c novice to delve deeply into the core of htslib. This could perhaps be done better using
bcf_hdr_get_hrec.In the end I made a short function to filter down the
HeaderRecord vectorusing anIDvalue. Since there should only ever be one INFO header record with a particular ID, I return the description from the first of the remaining records. If it's not there I pass along the default value. On the way out I make sure to trim the"since theupdate_headerfunction expects the descriptions to be unquoted.In the
encoder_mainfunction I only call this function when thefielddescriptionis not the default. I figure we'd want to give user priority in field naming.As for how the check against the default is done, I couldn't really figure out how to get a default value for a field the way things were so I went ahead and made the
fields::default_description_string()function public. I'm not sure if that's a good way of doing that so I'm open to suggestions.Let me know if this is fine. Feel free to discard the PR if you want to go about this a different way.