Merge pull request #30 from COMBINE-lab/dev

Dev

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "oarfish"
-version = "0.6.0"
+version = "0.6.1"
 edition = "2021"
 authors = [
   "Zahra Zare Jousheghani <[email protected]>",
@@ -60,7 +60,7 @@ crossbeam = { version = "0.8.4", features = [
 sprs = "0.11.1"
 minimap2-sys = { version = "0.1.19" }
 # rely on minimap2-temp until upstream version is pushed
-minimap2-temp = { version = "0.1.30" }
+minimap2-temp = { version = "0.1.31" }
 # alternative sources for dev
 #git = "https://github.com/rob-p/minimap2-rs.git", branch = "alignment-score" }
 #git = "https://github.com/jguhlin/minimap2-rs.git", branch = "alignment-score" }

src/util/aux_counts.rs

@@ -6,6 +6,7 @@ use itertools::izip;
 pub struct CountInfo {
     pub unique_count: u32,
     pub total_count: u32,
+    #[allow(dead_code)]
     pub expected_count: f64,
 }
 

src/util/oarfish_types.rs

@@ -262,8 +262,11 @@ impl<T: sam::alignment::record::Record> From<&T> for AlnInfo {
 #[serde(rename_all = "PascalCase")]
 pub struct ShortReadRecord {
     pub name: String,
+    #[allow(dead_code)]
     pub length: i32,
+    #[allow(dead_code)]
     pub effective_length: f64,
+    #[allow(dead_code)]
     #[serde(rename = "TPM")]
     pub tpm: f64,
     pub num_reads: f64,