progresss

src/variants.rs

@@ -591,12 +591,20 @@ impl Variants {
         Ok(())
     }
 
-    ///
+    /// Merge identical variants (same position, reference and alternative).
     pub fn merge(&mut self) {
-        let pg = self.mp.add(new_pg_speed(self.len() as u64));
-        pg.set_message("Merging Variants by contig, positions, ref, alt");
+        let reporter_msg =
+            "Merging identical variants (same position, reference and alternative)".to_string();
+        info!("{reporter_msg}");
+        if self.reporter.with_multi_progress {
+            self.reporter
+                .create_counter(&reporter_msg, Some(self.len() as u64));
+        } else {
+            self.reporter.create_counter(&reporter_msg, None);
+        }
+
         let hm: DashMap<String, Variant> = DashMap::new();
-        self.data.par_iter().progress_with(pg).for_each(|e| {
+        self.data.par_iter().for_each(|e| {
             let k = format!(
                 "{}:{}|{}>{}",
                 e.contig, e.position, e.reference, e.alternative
@@ -613,6 +621,7 @@ impl Variants {
             } else {
                 hm.insert(k, e.clone());
             }
+            self.reporter.inc(&reporter_msg);
         });
         self.data = hm.iter().map(|e| e.value().clone()).collect();
     }
@@ -620,31 +629,39 @@ impl Variants {
     pub fn annotate_gff_feature(&mut self, gff_path: &str) -> Result<()> {
         let gff_path = gff_path.to_string();
         let len = self.data.len();
-        let pg = self.mp.add(new_pg_speed(self.len() as u64));
-        pg.set_message("GFF Annotate");
+        let gff_chunk_size = len / 33;
 
-        self.data
-            .par_chunks_mut(len / 33)
-            .progress_with(pg)
-            .for_each(|chunk| {
-                let mut reader = File::open(gff_path.to_string())
-                    .map(noodles_bgzf::Reader::new)
-                    .map(gff::Reader::new)
-                    .unwrap();
-
-                let index = noodles_csi::read(format!("{}.csi", gff_path)).unwrap();
-
-                for v in chunk.iter_mut() {
-                    let start = Position::try_from(v.position as usize).unwrap();
-                    let r = Region::new(v.contig.to_string(), start..=start);
-                    if let std::result::Result::Ok(rows) = reader.query(&index, &r.clone()) {
-                        for row in rows {
-                            let ncbi = NCBIGFF::try_from(row.unwrap()).unwrap();
-                            v.annotations.push(AnnotationType::NCBIGFF(ncbi));
-                        }
+        let reporter_msg = "GFF annotation".to_string();
+        info!("{reporter_msg}");
+        if self.reporter.with_multi_progress {
+            self.reporter.create_counter(
+                &reporter_msg,
+                Some((len as f64 / gff_chunk_size as f64) as u64),
+            );
+        } else {
+            self.reporter.create_counter(&reporter_msg, None);
+        }
+
+        self.data.par_chunks_mut(gff_chunk_size).for_each(|chunk| {
+            let mut reader = File::open(gff_path.to_string())
+                .map(noodles_bgzf::Reader::new)
+                .map(gff::Reader::new)
+                .unwrap();
+
+            let index = noodles_csi::read(format!("{}.csi", gff_path)).unwrap();
+
+            for v in chunk.iter_mut() {
+                let start = Position::try_from(v.position as usize).unwrap();
+                let r = Region::new(v.contig.to_string(), start..=start);
+                if let std::result::Result::Ok(rows) = reader.query(&index, &r.clone()) {
+                    for row in rows {
+                        let ncbi = NCBIGFF::try_from(row.unwrap()).unwrap();
+                        v.annotations.push(AnnotationType::NCBIGFF(ncbi));
                     }
                 }
-            });
+            }
+            self.reporter.inc(&reporter_msg);
+        });
         Ok(())
     }