Merge pull request #3 from tedil/annotate

Add annotate functionality

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "cyrcular"
-version = "0.2.0"
-edition = "2018"
+version = "0.3.0"
+edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
@@ -10,7 +10,7 @@ bam = "0.1.4"
 anyhow = "1.0.70"
 itertools = "0.10.5"
 clap = { version = "4.2.1", features = ["derive"] }
-noodles = { version = "0.8", features = ["bcf", "vcf"] }
+noodles = { version = "0.28", features = ["bcf", "vcf", "bgzf"] }
 bio = "1.1.0"
 rayon = "1.7.0"
 indexmap = "1.9.3"
@@ -23,6 +23,7 @@ needletail = "0.5.1"
 statrs = "0.16.0"
 ordered-float = "3.6.0"
 lazy_static = "1.4.0"
+csv = "1.1.6"
 
 [dependencies.enumflags2]
 version = "0.7.6"
@@ -33,11 +34,11 @@ version = "0.6.3"
 features = ["serde-1"]
 
 [dependencies.serde]
-version = "1.0.159"
+version = "1.0.145"
 features = ["derive"]
 
 [dependencies.plotly]
-version = "0.7.0"
+version = "0.8.3"
 features = ["kaleido"]
 
 [dependencies.strum]

src/common.rs

@@ -105,9 +105,7 @@ impl<'a> SplitReadInfo<'a> {
                     dbg!(&record);
                     continue;
                 }
-                let tree = trees
-                    .entry(ref_id as u32)
-                    .or_insert_with(ArrayBackedIntervalTree::new);
+                let tree = trees.entry(ref_id as u32).or_default();
                 tree.insert(start..end, record);
             }
         }