fix: 0-1 alignment position issue in read-based mode

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "oarfish"
-version = "0.6.1"
+version = "0.6.2"
 edition = "2021"
 authors = [
   "Zahra Zare Jousheghani <[email protected]>",
@@ -25,7 +25,7 @@ categories = ["command-line-utilities", "science"]
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [dependencies]
-seqcol_rs = { git = "https://github.com/COMBINE-lab/seqcol_rs", branch = "dev", version = "0.1.0" }
+seqcol_rs = { git = "https://github.com/COMBINE-lab/seqcol_rs", branch = "dev", version = "0.1.2" }
 anyhow = "1.0.86"
 bio-types = { version = "1.0.4", features = ["serde"] }
 clap = { version = "4.5.16", features = ["derive"] }
@@ -51,7 +51,7 @@ arrow2 = { version = "0.18.0", features = [
   "io_parquet_zstd",
   "io_parquet_snappy",
 ] }
-kders = { git = "https://github.com/COMBINE-lab/kde-rs.git", branch = "dev", version = "0.1.0" }
+kders = { git = "https://github.com/COMBINE-lab/kde-rs.git", branch = "dev", version = "0.1.1" }
 noodles-bgzf = { version = "0.32.0" }
 crossbeam = { version = "0.8.4", features = [
   "crossbeam-queue",
@@ -63,7 +63,7 @@ minimap2-sys = { version = "0.1.19" }
 # make sure relevant changes are in upstream PR
 minimap2-temp = { version = "0.1.31" }
 # alternative sources for dev
-#git = "https://github.com/rob-p/minimap2-rs.git", branch = "alignment-score" }
+#minimap2 = { version = "0.1.20", git = "https://github.com/rob-p/minimap2-rs.git", branch = "alignment-score" }
 #git = "https://github.com/jguhlin/minimap2-rs.git", branch = "alignment-score" }
 needletail = "0.5.1"
 indicatif = "0.17.8"

src/util/oarfish_types.rs

@@ -140,11 +140,13 @@ impl AlnRecordLike for minimap2::Mapping {
     }
 
     fn aln_start(&self) -> u32 {
-        self.target_start.saturating_add(1) as u32
+        self.target_start as u32
     }
+
     fn aln_end(&self) -> u32 {
-        self.target_end.saturating_add(1) as u32
+        self.target_end as u32
     }
+
     fn is_supp(&self) -> bool {
         self.is_supplementary
     }