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69 lines
1.4 KiB
Markdown
69 lines
1.4 KiB
Markdown
# Progetto ASD 2023/2024
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## Usage
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- `cargo run -- --help`
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Display help message.
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- `cargo run -- show -i ./dataset/example.gfa`
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Parses the GFA file and prints the graph and various information.
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- Visualize the graph using EGUI, go to `examples/configurable` and run:
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`cargo run -- ../../dataset/example.gfa`
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`cargo run -- ../../dataset/DRB1-3123_unsorted.gfa`
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## Example GFA
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```
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H VN:Z:1.0
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S 11 G
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S 12 A
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S 13 T
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S 14 T
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S 15 A
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S 16 C
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S 17 A
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S 21 G
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S 22 A
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S 23 T
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S 24 T
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S 25 A
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L 11 + 12 + *
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L 11 + 13 + *
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L 12 + 14 + *
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L 13 + 14 + *
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L 14 + 15 + *
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L 14 + 16 + *
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L 15 + 17 + *
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L 16 + 17 + *
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L 21 + 22 + *
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L 21 + 23 + *
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L 22 + 24 + *
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L 23 + 24 - *
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L 24 + 25 + *
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P A 11+,12+,14+,15+,17+ *,*,*,*
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P B 21+,22+,24+,25+ *,*,*
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W sample 1 A 0 5 >11>12>14>15>17
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W sample 2 A 0 5 >11>13>14>16>17
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W sample 1 B 0 5 >21>22>24<23<21
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W sample 2 B 0 4 >21>22>24>25
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```
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## Note
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- Documentazione del formato GFA: http://gfa-spec.github.io/GFA-spec/GFA1.html
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- Data set:
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- [example.gfa](https://github.com/jltsiren/gbwt-rs/blob/main/test-data/example.gfa)
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- [drb1.gfa](https://github.com/pangenome/odgi/blob/master/test/DRB1-3123_unsorted.gfa)
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- [chrY.gfa](https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/pggb/chroms/chrY.hprc-v1.0-pggb.gfa.gz)
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- [chrX.gfa](https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/pggb/chroms/chrX.hprc-v1.0-pggb.gfa.gz)
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