Add command to propagate annotations #89
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dkhofer
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src/annotations/gff.rs
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| let mut path_mappings_by_name = HashMap::new(); | ||
| for (name, target_path) in target_paths_by_name.iter() { | ||
| let source_path = source_paths_by_name.get(name).unwrap(); |
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why do we assume the 2 sample groups need the same paths?
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The paths are associated with block group name (eg "chr22"). I just changed the variable names to make that clearer (eg source_paths_by_name -> source_paths_by_bg_name). So the two associated paths are the latest paths for block groups with the same name. Those pairs of paths are what we propagate annotations on. Let me know if I can do more to clarify that
| // Replaced (15, 25) with a 2 bp sequence | ||
| // New gene annotation is (5, 15) | ||
| assert_eq!(record.start().get(), 5); | ||
| assert_eq!(record.end().get(), 15); |
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what happens if we throw an insert into a gene? wondering if we split it up or just extend it.
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We "bridge" the annotation across the split up parts. The first check is on a region-wide annotation and confirms it still spans the region across a replaced part. I edited the comments to make that clearer. If you want a check on a gene annotation specifically, I can put one in
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