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Cargo.toml

@@ -0,0 +1,14 @@
+[package]
+name = "aligner_client"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+reqwest = { version = "0.12", features = ["json"] }
+tokio = { version = "1.36.0", features = ["full"] }
+minimap2 = { git = "https://github.com/jguhlin/minimap2-rs", features = ["htslib", "simde"]}
+serde = { version = "1.0.197", features = ["derive"] }
+serde_nested_with = "0.2.5"
+serde_json = "1.0.114"

src/lib.rs

@@ -0,0 +1,81 @@
+use std::num::NonZeroI32;
+use minimap2::{Alignment, Strand, Mapping};
+use serde::{Serialize, Deserialize};
+use serde_nested_with::serde_nested;
+
+pub async fn get_mappings(url: &str, sequence: String) -> Result<Mappings, Box<dyn std::error::Error>> {
+    let client = reqwest::Client::new();
+    let url = reqwest::Url::parse(url)?;
+
+    let response = client.post(url).body(sequence).send().await?;
+    let response_body = response.text().await?;
+    let mappings: Mappings = serde_json::from_str(&response_body)?;
+
+    Ok(mappings)
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+#[serde(remote = "Strand")]
+enum StrandDef {
+    Forward,
+    Reverse,
+}
+
+#[derive(Serialize, Deserialize, Debug)]
+#[serde(remote = "Alignment")]
+struct AlignmentDef {
+    pub nm: i32,
+    pub cigar: Option<Vec<(u32, u8)>>,
+    pub cigar_str: Option<String>,
+    pub md: Option<String>,
+    pub cs: Option<String>,
+}
+
+#[serde_nested]
+#[derive(Serialize, Deserialize, Debug)]
+#[serde(remote = "Mapping")]
+pub struct MappingDef {
+    query_name: Option<String>,
+    query_len: Option<NonZeroI32>,
+    query_start: i32,
+    query_end: i32,
+    #[serde(with = "StrandDef")]
+    strand: Strand,
+    target_name: Option<String>,
+    target_len: i32,
+    target_start: i32,
+    target_end: i32,
+    match_len: i32,
+    block_len: i32,
+    mapq: u32,
+    is_primary: bool,
+    is_supplementary: bool,
+    #[serde_nested(sub = "Alignment", serde(with = "AlignmentDef"))]
+    alignment: Option<Alignment>,
+}
+
+#[serde_nested]
+#[derive(Debug, PartialEq, Eq, Serialize, Deserialize)]
+pub struct Mappings {
+    #[serde_nested(
+        sub = "Mapping",
+        serde(
+            serialize_with = "MappingDef::serialize",
+            deserialize_with = "MappingDef::deserialize"
+        )
+    )]
+    pub inner: Vec<Mapping>,
+}
+
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[tokio::test]
+    async fn it_works() {
+        let mut mappings = get_mappings("http://localhost:4444/align", "ACCAAAACACATATTCACGGCAGCCACTCCACCCAGCACCTCaca".to_string()).await.unwrap();
+        let mapping = mappings.inner.pop().unwrap();
+        assert_eq!(mapping.target_name.unwrap(), "chr6".to_string());
+    }
+}