diff --git a/Cargo.toml b/Cargo.toml index 40b8b56..e4b60a2 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "oarfish" -version = "0.6.1" +version = "0.6.2" edition = "2021" authors = [ "Zahra Zare Jousheghani ", @@ -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" diff --git a/src/util/oarfish_types.rs b/src/util/oarfish_types.rs index 988c8f5..39217d7 100644 --- a/src/util/oarfish_types.rs +++ b/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 }