mirror of https://github.com/aziis98/asd-2024.git
initial commit
commit
c897945e06
@ -0,0 +1,5 @@
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# Cargo
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/target
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# Local files
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*.local*
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@ -0,0 +1,96 @@
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# This file is automatically @generated by Cargo.
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# It is not intended for manual editing.
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version = 3
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[[package]]
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name = "argh"
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version = "0.1.12"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "7af5ba06967ff7214ce4c7419c7d185be7ecd6cc4965a8f6e1d8ce0398aad219"
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dependencies = [
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"argh_derive",
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"argh_shared",
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]
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[[package]]
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name = "argh_derive"
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version = "0.1.12"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "56df0aeedf6b7a2fc67d06db35b09684c3e8da0c95f8f27685cb17e08413d87a"
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dependencies = [
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"argh_shared",
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"proc-macro2",
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"quote",
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"syn",
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]
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[[package]]
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name = "argh_shared"
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version = "0.1.12"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "5693f39141bda5760ecc4111ab08da40565d1771038c4a0250f03457ec707531"
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dependencies = [
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"serde",
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]
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[[package]]
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name = "asd-2024-gfa"
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version = "0.1.0"
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dependencies = [
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"argh",
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]
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[[package]]
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name = "proc-macro2"
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version = "1.0.83"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "0b33eb56c327dec362a9e55b3ad14f9d2f0904fb5a5b03b513ab5465399e9f43"
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dependencies = [
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"unicode-ident",
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]
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[[package]]
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name = "quote"
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version = "1.0.36"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7"
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dependencies = [
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"proc-macro2",
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]
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[[package]]
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name = "serde"
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version = "1.0.202"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "226b61a0d411b2ba5ff6d7f73a476ac4f8bb900373459cd00fab8512828ba395"
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dependencies = [
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"serde_derive",
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]
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[[package]]
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name = "serde_derive"
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version = "1.0.202"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "6048858004bcff69094cd972ed40a32500f153bd3be9f716b2eed2e8217c4838"
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dependencies = [
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"proc-macro2",
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"quote",
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"syn",
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]
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[[package]]
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name = "syn"
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version = "2.0.65"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "d2863d96a84c6439701d7a38f9de935ec562c8832cc55d1dde0f513b52fad106"
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dependencies = [
|
||||
"proc-macro2",
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"quote",
|
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"unicode-ident",
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]
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[[package]]
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name = "unicode-ident"
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version = "1.0.12"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
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@ -0,0 +1,7 @@
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[package]
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name = "asd-2024-gfa"
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version = "0.1.0"
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edition = "2021"
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[dependencies]
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argh = "0.1.12"
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@ -0,0 +1,48 @@
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# Progetto ASD 2023/2024
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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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@ -0,0 +1,32 @@
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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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@ -0,0 +1,40 @@
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use argh::FromArgs;
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mod parser;
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#[derive(FromArgs, PartialEq, Debug)]
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/// Strumento CLI per il progetto di Algoritmi e Strutture Dati 2024
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struct CliTool {
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#[argh(subcommand)]
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nested: MySubCommandEnum,
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}
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#[derive(FromArgs, PartialEq, Debug)]
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#[argh(subcommand)]
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enum MySubCommandEnum {
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Show(CommandShow),
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}
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#[derive(FromArgs, PartialEq, Debug)]
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/// Parse and show the content of a file
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#[argh(subcommand, name = "show")]
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struct CommandShow {
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#[argh(option, short = 'i')]
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/// file to read
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input: String,
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}
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fn main() {
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let opts = argh::from_env::<CliTool>();
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match opts.nested {
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MySubCommandEnum::Show(show) => {
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let file = std::fs::read_to_string(show.input).expect("cannot read file");
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let entries = parser::parse_source(file.as_str());
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for entry in entries {
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println!("{:?}", entry);
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}
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}
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}
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}
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@ -0,0 +1,184 @@
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use std::str::FromStr;
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#[derive(Debug)]
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pub enum Orientation {
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Forward,
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Reverse,
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}
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impl From<&str> for Orientation {
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fn from(s: &str) -> Self {
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match s {
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"+" => Orientation::Forward,
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">" => Orientation::Forward,
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"-" => Orientation::Reverse,
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"<" => Orientation::Reverse,
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_ => panic!("Invalid orientation: {}", s),
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}
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}
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}
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#[derive(Debug)]
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pub enum Entry {
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Header {
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version: String,
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},
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Segment {
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id: String,
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sequence: String,
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},
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Link {
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from: String,
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from_orient: Orientation,
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to: String,
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to_orient: Orientation,
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},
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Path {
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name: String,
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segments: Vec<(String, Orientation)>,
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},
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Walk {
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sample: String,
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haplotype_index: usize,
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seq_id: String,
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seq_start: usize,
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seq_end: usize,
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segments: Vec<(String, Orientation)>,
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},
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}
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/// Parse a line of the source file into a Header struct
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///
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/// ```txt
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/// H VN:Z:1.0
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/// ```
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///
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fn parse_header(line: &str) -> Entry {
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let columns: Vec<&str> = line.split(':').collect();
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Entry::Header {
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version: columns[2].to_string(),
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}
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}
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/// Parse a line of the source file into a Segment struct
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///
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/// ```txt
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/// S 1 ACGT
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/// ```
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fn parse_segment(line: &str) -> Entry {
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let columns: Vec<&str> = line.split('\t').collect();
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Entry::Segment {
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id: columns[1].to_string(),
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sequence: columns[2].to_string(),
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}
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}
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/// Parse a line of the source file into a Link struct
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///
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/// ```txt
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/// L 1 + 2 - 3M
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/// ```
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fn parse_link(line: &str) -> Entry {
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let columns: Vec<&str> = line.split('\t').collect();
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Entry::Link {
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from: columns[1].to_string(),
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from_orient: columns[2].into(),
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to: columns[3].to_string(),
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to_orient: columns[4].into(),
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}
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}
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/// Parse a line of the source file into a Path struct
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///
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/// ```txt
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/// P A 11+,12+,14+,15-,17+ *,*,*,*
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/// ```
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fn parse_path(line: &str) -> Entry {
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let columns: Vec<&str> = line.split('\t').collect();
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Entry::Path {
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name: columns[1].to_string(),
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segments: columns[2]
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.split(',')
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.map(|s| {
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let (name, orient) = s.split_at(s.len() - 1);
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(name.to_string(), orient.into())
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})
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.collect(),
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}
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}
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fn parse_path_segments(s: &str) -> Vec<(String, Orientation)> {
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let mut result = Vec::new();
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let mut rest = s;
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loop {
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println!("Rest: {}", rest);
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let r = rest;
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let (orient, r) = r.split_at(1);
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let (name, r) = r.split_at(r.find(['<', '>']).unwrap_or(r.len()));
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rest = r;
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result.push((name.to_string(), orient.into()));
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if rest.is_empty() {
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break;
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}
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}
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result
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}
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/// Parse a line of the source file into a Walk struct
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///
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/// ```txt
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/// W sample 1 A 0 5 >11>12>14>15>17
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/// ```
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fn parse_walk(line: &str) -> Entry {
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let columns: Vec<&str> = line.split('\t').collect();
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Entry::Walk {
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sample: columns[1].to_string(),
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|
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haplotype_index: usize::from_str(columns[2]).unwrap(),
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seq_id: columns[3].to_string(),
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seq_start: usize::from_str(columns[4]).unwrap(),
|
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seq_end: usize::from_str(columns[5]).unwrap(),
|
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|
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segments: parse_path_segments(columns[6]),
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}
|
||||
}
|
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|
||||
pub fn parse_source(source: &str) -> Vec<Entry> {
|
||||
let mut entries = Vec::new();
|
||||
for line in source.lines() {
|
||||
let line = line.trim();
|
||||
if line.is_empty() || line.starts_with('#') {
|
||||
continue;
|
||||
}
|
||||
|
||||
println!("Parsing: {}", line);
|
||||
|
||||
let first_char = line.chars().next().unwrap();
|
||||
let entry = match first_char {
|
||||
'H' => parse_header(line),
|
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'S' => parse_segment(line),
|
||||
'L' => parse_link(line),
|
||||
'P' => parse_path(line),
|
||||
'W' => parse_walk(line),
|
||||
_ => {
|
||||
eprintln!("Unknown line type: {}", line);
|
||||
continue;
|
||||
}
|
||||
};
|
||||
entries.push(entry);
|
||||
}
|
||||
entries
|
||||
}
|
||||
Loading…
Reference in New Issue