Update CI version of rust.

Run cargo clippy --fix.

Author: adam-azarchs

.github/workflows/test.yml

@@ -17,7 +17,7 @@ jobs:
     steps:
       - uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.58.1
+          toolchain: 1.59.0
           components: rustfmt, clippy
           default: true
       - name: Checkout git repository

ansi_escape/src/ansi_to_html.rs

@@ -238,7 +238,7 @@ pub fn compress_ansi_escapes(x: &str) -> String {
                         for e in escapes.iter() {
                             if e.solo() && e[0] == 1 {
                                 if reset || new_state.bold != old_state.bold {
-                                    out += &strme(&pack_ansi_escape(e)).to_string();
+                                    out += strme(&pack_ansi_escape(e));
                                 }
                                 break;
                             }
@@ -249,7 +249,7 @@ pub fn compress_ansi_escapes(x: &str) -> String {
                                 || (y.len() == 3 && y[0] == 38 && y[1] == 5)
                             {
                                 if reset || new_state.color != old_state.color {
-                                    out += &strme(&pack_ansi_escape(y)).to_string();
+                                    out += strme(&pack_ansi_escape(y));
                                 }
                                 break;
                             }
@@ -260,7 +260,7 @@ pub fn compress_ansi_escapes(x: &str) -> String {
                                 || (y.len() == 3 && y[0] == 48 && y[1] == 5)
                             {
                                 if reset || new_state.background != old_state.background {
-                                    out += &strme(&pack_ansi_escape(y)).to_string();
+                                    out += strme(&pack_ansi_escape(y));
                                 }
                                 break;
                             }
@@ -404,7 +404,7 @@ impl ColorState {
                 s += &format!("background-color:{};", self.background);
             }
             if self.bold {
-                s += &"font-weight:bold;".to_string()
+                s += "font-weight:bold;"
             }
             s += "\">";
             s
@@ -422,7 +422,7 @@ impl ColorState {
                 s += &format!("fill: {};", self.color);
             }
             if self.bold {
-                s += &"font-weight: bold;".to_string()
+                s += "font-weight: bold;"
             }
             s += "\">";
             s

fasta_tools/src/lib.rs

@@ -195,6 +195,6 @@ pub fn load_genbank_accession(accession: &str, bases: &mut DnaString) {
     // ◼ The following assert should not be necessary: the DnaString constructor
     // ◼ should gag if it gets nonsense input.
     assert!(!fasta.contains("moved"));
-    fasta = fasta.replace("\n", "");
+    fasta = fasta.replace('\n', "");
     *bases = DnaString::from_dna_string(&fasta);
 }

perf_stats/src/lib.rs

@@ -40,8 +40,8 @@ pub fn nthreads() -> i64 {
                 let s = line.unwrap();
                 if s.starts_with("Threads:") {
                     let mut s = s.after("Threads:").to_string();
-                    s = s.replace("\t", "");
-                    s = s.replace(" ", "");
+                    s = s.replace('\t', "");
+                    s = s.replace(' ', "");
                     return s.force_i64();
                 }
             }
@@ -229,7 +229,7 @@ pub fn ps_me() {
                 ppid = s.after("PPid:\t").force_i64();
             } else if s.starts_with("VmRSS:\t") {
                 let t = s.after("VmRSS:\t");
-                let t = t.to_string().replace(" ", "");
+                let t = t.to_string().replace(' ', "");
                 rss = t.before("k").force_f64() / (1024 * 1024) as f64;
             }
         }
@@ -245,7 +245,7 @@ pub fn ps_me() {
                 continue 'outer;
             } // fail that does occur rarely
             cmd = line.unwrap();
-            cmd = cmd.replace("
+            cmd = cmd.replace('
         }
         if cmd.len() <= RIGHT {
             println!("{:6}  {:6} {:7.2}  {}", ppid, pid, rss, cmd);

pretty_trace/src/lib.rs

@@ -306,7 +306,7 @@ pub fn stop_profiling() {
             }
             if !symv.is_empty() {
                 let mut log = String::new();
-                print_tabular_vbox(&mut log, &symv, 0, &b"l|l|l|l|l".to_vec(), false, false);
+                print_tabular_vbox(&mut log, &symv, 0, b"l|l|l|l|l".as_ref(), false, false);
                 for _ in 0..*count {
                     let x = log.to_string();
                     traces.push(x);

vdj_ann/src/annotate.rs

@@ -3344,7 +3344,7 @@ mod tests {
         let annotation = ContigAnnotation::from_seq(
             &contig_seq,
             &contig_qual,
-            &"clonotype125_consensus_1".to_string(),
+            "clonotype125_consensus_1",
             &refdata,
             120,
             2,

vdj_ann/src/vdj_features.rs

@@ -679,7 +679,7 @@ pub fn score_fwr3(aa: &[u8], r: usize, freqs: &[Vec<Vec<(u32, u8)>>]) -> f64 {
     } else {
         chain_type = "TRB";
     }
-    let cdr3 = cdr3_start(&aa.to_vec(), chain_type, false);
+    let cdr3 = cdr3_start(aa, chain_type, false);
     let motif = freqs[0].len();
     let mut score = 0.0;
     for j in 0..motif {
@@ -736,7 +736,7 @@ pub fn score4(aa: &[u8], r: usize) -> usize {
     } else {
         chain_type = "TRB";
     }
-    let cdr3 = cdr3_start(&aa.to_vec(), chain_type, false);
+    let cdr3 = cdr3_start(aa, chain_type, false);
     let n = aa.len();
     assert!(n >= 22);
     let mut score = 0;

vdj_ann_ref/src/bin/build_supp_ref.rs

@@ -66,7 +66,7 @@ fn main() {
     // Load the exons.
 
     let mut exons = Vec::<(String, i32, i32, bool, String, i32)>::new();
-    fetch_exons(&species.to_string(), &mut exons);
+    fetch_exons(species, &mut exons);
 
     // Hardcoded and inappropriate fasta location.
     // source = ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/
@@ -168,10 +168,10 @@ fn main() {
         if i > 0 && *chr == exons2[i - 1].0 && gap < MIN_EXTRA as i32 {
             continue;
         }
-        if !to_chr.contains_key(&chr.to_string()) {
+        if !to_chr.contains_key(chr) {
             continue;
         }
-        let chrid = to_chr[&chr.to_string()];
+        let chrid = to_chr[chr];
 
         // Case 1.  Gap is not too long, use it all.  Create sequence and emit as
         // rust code.  Then code the rc.

vdj_ann_ref/src/bin/build_vdj_ref.rs

@@ -1173,7 +1173,7 @@ fn main() {
         if gene2.contains('(') {
             gene2 = gene2.before("(").to_string();
         }
-        gene2 = gene2.replace(" ", "");
+        gene2 = gene2.replace(' ', "");
         if gene2.contains("identical") || gene2.contains("identicle") {
             continue;
         }
@@ -1260,7 +1260,7 @@ fn main() {
     let mut dna = Vec::<DnaString>::new();
     for i in 0..exons.len() {
         let chr = &exons[i].2;
-        let chrid = to_chr[&chr.to_string()];
+        let chrid = to_chr[chr];
         let (start, stop) = (exons[i].3, exons[i].4);
         let seq = refs[chrid].slice(start as usize, stop as usize).to_owned();
         dna.push(seq);

vdj_ann_ref/src/bin/build_vdj_ref_exons.rs

@@ -824,7 +824,7 @@ fn main() {
         if gene2.contains('(') {
             gene2 = gene2.before("(").to_string();
         }
-        gene2 = gene2.replace(" ", "");
+        gene2 = gene2.replace(' ', "");
         if gene2.contains("identical") || gene2.contains("identicle") {
             continue;
         }
@@ -912,7 +912,7 @@ fn main() {
     let mut stops = Vec::<usize>::new();
     for i in 0..exons.len() {
         let chr = &exons[i].2;
-        let chrid = to_chr[&chr.to_string()];
+        let chrid = to_chr[chr];
         starts.push(exons[i].3 as usize);
         stops.push(exons[i].4 as usize);
         let (start, stop) = (exons[i].3 - EXT as i32, exons[i].4 + EXT as i32);