GFA import #6
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GFA import #6
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Chris7
approved these changes
Jul 29, 2024
Cargo.toml
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| @@ -6,6 +6,7 @@ edition = "2021" | |||
| [dependencies] | |||
| bio = "2.0.0" | |||
| clap = { version = "4.5.8", features = ["derive"] } | |||
| gfa-reader = { git = "https://github.com/MoinSebi/gfa-reader", branch = "master" } | |||
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Yep, just added that
Chris7
approved these changes
Sep 6, 2024
| .sequence_type("DNA") | ||
| .sequence(input_sequence) | ||
| .save(conn); | ||
| sequences_by_segment_id.insert(segment.id, sequence); |
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we'll probably need to trim this out at larger scale as we won't be able to store all the sequences in memory
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| for segment in &gfa.segments { | ||
| let input_sequence = segment.sequence.get_string(&gfa.sequence); | ||
| let sequence = Sequence::new() |
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what would a shallow version of this look like?
| let mut source_hash = Sequence::PATH_START_HASH; | ||
| let mut source_coordinate = 0; | ||
| let mut path_edge_ids = vec![]; | ||
| for segment_id in input_walk.walk_id.iter() { |
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does this bring any of the strand info with it? walks do have direction
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I was being lazy. I'll check what the parser provides and deal with it in a followup PR
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