update

Cargo.toml

@@ -4,12 +4,10 @@ version = "0.1.0"
 edition = "2021"
 
 [dependencies]
-log = "^0.4.22"
-env_logger = "^0.11.3"
-anyhow = "1.0.86"
+log = "^0.4.29"
+env_logger = "^0.11.8"
+anyhow = "1.0.100"
 glob = "0.3.2"
-pandora_lib_scan = { git = "https://git.t0m4.fr/Thomas/pandora_lib_scan.git" }
-pandora_lib_variants = { git = "https://git.t0m4.fr/Thomas/pandora_lib_variants.git" }
 pandora_lib_assembler = { git = "https://git.t0m4.fr/Thomas/pandora_lib_assembler.git" }
 chrono = { version = "0.4.40", features = ["serde"] }
 csv = "1.3.0"
@@ -20,7 +18,7 @@ noodles-csi = "0.53.0"
 num-format = "0.4.4"
 byte-unit = "5.1.4"
 uuid = { version = "1.13.1", features = ["v4"] }
-rayon = "1.10.0"
+rayon = "1.11.0"
 hashbrown = { version = "0.16.1", features = ["rayon"] }
 lazy_static = "1.5.0"
 indicatif = "0.17.8"
@@ -31,12 +29,12 @@ bgzip = "0.3.1"
 dashmap = { version = "6.1.0", features = ["rayon", "serde"] }
 noodles-fasta = "0.58.0"
 noodles-core = "0.18.0"
-blake3 = "1.5.5"
-rusqlite = { version = "0.33.0", features = ["chrono", "serde_json"] }
+blake3 = "1.8.2"
+rusqlite = { version = "0.38.0", features = ["chrono", "serde_json"] }
 dirs = "6.0.0"
 noodles-gff = "0.54.0"
 itertools = "0.14.0"
-rand = "0.9.0"
+rand = "0.9.2"
 tar = "0.4.43"
 flatbuffers = "25.2.10"
 ordered-float = { version = "5.0.0", features = ["serde"] }

src/commands/longphase.rs

@@ -471,7 +471,7 @@ impl crate::commands::SbatchRunner for LongphasePhase {
         crate::commands::SlurmParams {
             job_name: Some(format!("longphase_phase_{}", self.id)),
             cpus_per_task: Some(self.config.longphase_threads as u32),
-            mem: Some("60G".into()),
+            mem: Some("90G".into()),
             partition: Some("shortq".into()),
             gres: None,
         }

src/functions/mod.rs

@@ -1,4 +1,2 @@
-pub mod whole_scan;
-pub mod variants;
 pub mod assembler;
 pub mod fb_inv_stats;

src/functions/variants.rs

@@ -1,33 +0,0 @@
-use indicatif::MultiProgress;
-use pandora_lib_variants::variants;
-
-#[derive(Debug, Clone)]
-pub struct VariantsConfig {
-    pub result_dir: String,
-}
-
-impl Default for VariantsConfig {
-    fn default() -> Self {
-        Self {
-            result_dir: "/data/longreads_basic_pipe".to_string(),
-        }
-    }
-}
-
-#[derive(Debug)]
-pub struct RunVariantsAgg {
-    pub id: String,
-    pub config: VariantsConfig,
-}
-
-impl RunVariantsAgg {
-    pub fn new(id: String, config: VariantsConfig) -> Self {
-        Self { id, config }
-    }
-    pub fn run(&self) -> anyhow::Result<()> {
-        let multi = MultiProgress::default();
-        // multi.suspend(|| {
-        variants::run_pipe(&self.id, true, &multi)
-        // });
-    }
-}

src/functions/whole_scan.rs

@@ -1,50 +0,0 @@
-use pandora_lib_scan::par_whole_scan;
-
-#[derive(Debug, Clone)]
-pub struct WholeScanConfig {
-    pub result_dir: String,
-    pub scan_dir: String,
-    pub dict_file: String,
-}
-
-impl Default for WholeScanConfig {
-    fn default() -> Self {
-        Self {
-            result_dir: "/data/longreads_basic_pipe".to_string(),
-            scan_dir: "scan".to_string(),
-            dict_file: "".to_string(),
-        }
-    }
-}
-
-#[derive(Debug)]
-pub struct WholeScan {
-    pub id: String,
-    pub time_point: String,
-    pub bam_path: String,
-    pub config: WholeScanConfig,
-}
-
-impl WholeScan {
-    pub fn new(
-        id: String,
-        time_point: String,
-        bam_path: String,
-        config: WholeScanConfig
-    ) -> anyhow::Result<Self> {
-        Ok(WholeScan {
-            id,
-            time_point,
-            config,
-            bam_path,
-        })
-    }
-    pub fn run(&self) -> anyhow::Result<()> {
-        let scan_dir = format!(
-            "{}/{}/{}/{}",
-            &self.config.result_dir, self.id, self.time_point, self.config.scan_dir
-        );
-        par_whole_scan(&self.config.dict_file, &self.bam_path, &scan_dir)?;
-        Ok(())
-    }
-}