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Bump rust version and transitive deps. #65

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merged 3 commits into from
Mar 30, 2022
Merged

Bump rust version and transitive deps. #65

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835eca7
Bump rust version to 1.59.0.
adam-azarchs Mar 26, 2022
3d4a5c2
Update transitive dependencies.
adam-azarchs Mar 26, 2022
293701b
explicit dep on libz-sys
luiz10x Mar 30, 2022
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2 changes: 1 addition & 1 deletion .github/workflows/release.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ jobs:
- name: Install Rust
uses: actions-rs/toolchain@v1
with:
toolchain: 1.58.1
toolchain: 1.59.0
default: true
- name: Make release build
run: |
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4 changes: 2 additions & 2 deletions .github/workflows/test.yaml
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Expand Up @@ -17,7 +17,7 @@ jobs:
- name: Install Rust
uses: actions-rs/toolchain@v1
with:
toolchain: 1.58.1
toolchain: 1.59.0
components: rustfmt
default: true
- name: Checkout bamtofastq master
Expand All @@ -36,7 +36,7 @@ jobs:
- name: Install Rust
uses: actions-rs/toolchain@v1
with:
toolchain: 1.58.1
toolchain: 1.59.0
components: rustfmt, clippy
default: true
- name: Checkout bamtofastq master
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65 changes: 33 additions & 32 deletions Cargo.lock
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1 change: 1 addition & 0 deletions Cargo.toml
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Expand Up @@ -20,6 +20,7 @@ curl = ["rust-htslib/curl"]
docopt = "*"
rust-htslib = { version = "0.38", default-features = false }
flate2 = { version = "1.0", features = ["zlib"], default-features = false }
libz-sys = "1.1.5"
shardio = "0.8.2"
bincode = "1"
itertools = ">=0.8.0"
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2 changes: 1 addition & 1 deletion src/locus.rs
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Expand Up @@ -21,7 +21,7 @@ impl fmt::Display for Locus {

fn remove_commas(s: &str) -> String {
let ss = s.to_string();
ss.replace(",", "")
ss.replace(',', "")
}

impl FromStr for Locus {
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6 changes: 3 additions & 3 deletions src/main.rs
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Expand Up @@ -214,8 +214,8 @@ impl FormatBamRecords {
rg_spec: rgs,
r1_spec: spec.remove("R1").unwrap(),
r2_spec: spec.remove("R2").unwrap(),
i1_spec: spec.remove("I1").unwrap_or_else(Vec::new),
i2_spec: spec.remove("I2").unwrap_or_else(Vec::new),
i1_spec: spec.remove("I1").unwrap_or_default(),
i2_spec: spec.remove("I2").unwrap_or_default(),
rename: seq_names,
order: [1, 3, 2, 4],
})
Expand Down Expand Up @@ -668,7 +668,7 @@ impl FastqManager {
for (_, &(ref _samp, lane)) in formatter.rg_spec.iter() {
let samp = _samp.clone();
let path = sample_def_paths.entry(samp).or_insert_with(|| {
let suffix = _samp.replace(":", "_");
let suffix = _samp.replace(':', "_");

//create_dir(&samp_path).expect("couldn't create output directory");
out_path.join(suffix)
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