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Dev #30

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merged 3 commits into from
Aug 26, 2024
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Dev #30

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a707160
Merge pull request #28 from COMBINE-lab/main
rob-p Aug 26, 2024
055bfc7
Merge pull request #29 from COMBINE-lab/main
rob-p Aug 26, 2024
9877d94
bump minimap2-temp crate
Aug 26, 2024
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4 changes: 2 additions & 2 deletions Cargo.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[package]
name = "oarfish"
version = "0.6.0"
version = "0.6.1"
edition = "2021"
authors = [
"Zahra Zare Jousheghani <[email protected]>",
Expand Down Expand Up @@ -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" }
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1 change: 1 addition & 0 deletions src/util/aux_counts.rs
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Expand Up @@ -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,
}

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3 changes: 3 additions & 0 deletions src/util/oarfish_types.rs
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Expand Up @@ -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,
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