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adam-azarchsadam-azarchs
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build: bump rust to 1.68 and fix new clippy lints
1 parent b54945c commit 5457751

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10 files changed

+41
-43
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10 files changed

+41
-43
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Diff for: ‎.github/workflows/test.yml

+4-4
Original file line numberDiff line numberDiff line change
@@ -17,18 +17,18 @@ jobs:
1717
steps:
1818
- uses: dtolnay/rust-toolchain@master
1919
with:
20-
toolchain: 1.65.0
20+
toolchain: 1.68.0
2121
components: rustfmt, clippy
2222
- name: Checkout git repository
2323
uses: actions/checkout@master
2424
- name: Check Rust formatting
2525
run: cargo fmt -- --check
2626
- name: Install cargo-deny
2727
run: |
28-
wget https://github.com/EmbarkStudios/cargo-deny/releases/download/0.13.5/cargo-deny-0.13.5-x86_64-unknown-linux-musl.tar.gz
29-
tar -xvf cargo-deny-0.13.5-x86_64-unknown-linux-musl.tar.gz
28+
wget https://github.com/EmbarkStudios/cargo-deny/releases/download/0.13.7/cargo-deny-0.13.7-x86_64-unknown-linux-musl.tar.gz
29+
tar -xvf cargo-deny-0.13.7-x86_64-unknown-linux-musl.tar.gz
3030
mkdir -p ~/bin/
31-
cp cargo-deny-0.13.5-x86_64-unknown-linux-musl/cargo-deny ~/bin/
31+
cp cargo-deny-0.13.7-x86_64-unknown-linux-musl/cargo-deny ~/bin/
3232
rm -r cargo-deny-*
3333
echo "$HOME/bin" >> $GITHUB_PATH
3434
- name: Cache cargo registry

Diff for: ‎equiv/src/lib.rs

+2-2
Original file line numberDiff line numberDiff line change
@@ -95,7 +95,7 @@ impl EquivRel {
9595
pub fn orbit_reps(&self, reps: &mut Vec<i32>) {
9696
reps.clear();
9797
for i in 0..self.x.len() {
98-
if i == self.y[i as usize] as usize {
98+
if i == self.y[i] as usize {
9999
reps.push(i as i32);
100100
}
101101
}
@@ -104,7 +104,7 @@ impl EquivRel {
104104
pub fn norbits(&self) -> usize {
105105
let mut n = 0;
106106
for i in 0..self.x.len() {
107-
if i == self.y[i as usize] as usize {
107+
if i == self.y[i] as usize {
108108
n += 1;
109109
}
110110
}

Diff for: ‎hyperbase/src/lib.rs

+6-6
Original file line numberDiff line numberDiff line change
@@ -277,8 +277,8 @@ impl Hyper {
277277
println!("\nCOMPONENT {}", j + 1);
278278
for i in 0..comp[j].len() {
279279
let e = comp[j][i];
280-
let v = self.h.g.to_left(e as u32);
281-
let w = self.h.g.to_right(e as u32);
280+
let v = self.h.g.to_left(e);
281+
let w = self.h.g.to_right(e);
282282
let b: DnaString = self.h.g[EdgeIndex::<u32>::new(e as usize)].clone();
283283
println!(
284284
"\n{} ==(e={},len={},supp={})==> {}",
@@ -634,7 +634,7 @@ impl Hyper {
634634
break;
635635
}
636636
}
637-
if eleft < self.inv[eright as usize] as usize {
637+
if eleft < self.inv[eright] as usize {
638638
bound.push((eleft as u32, eright as u32));
639639
bound.push((self.inv[eright], self.inv[eleft]));
640640
}
@@ -671,8 +671,8 @@ impl Hyper {
671671
}
672672
let edge_id = self.h.g.first_edge(v, Outgoing).unwrap();
673673
let edge = self.h.g[edge_id].clone();
674-
for j in 0..self.ids[edge_id.index() as usize].len() {
675-
let id = self.ids[edge_id.index() as usize][j];
674+
for j in 0..self.ids[edge_id.index()].len() {
675+
let id = self.ids[edge_id.index()][j];
676676
if !havex[id as usize] {
677677
have.push(id);
678678
havex[id as usize] = true;
@@ -752,7 +752,7 @@ impl Hyper {
752752
);
753753
panic!("Involution test failed.");
754754
}
755-
assert_eq!(self.inv[self.inv[e as usize] as usize], e as u32);
755+
assert_eq!(self.inv[self.inv[e] as usize], e as u32);
756756
let t = self.h.g[EdgeIndex::<u32>::new(e)].rc().to_string();
757757
assert_eq!(
758758
self.h.g[EdgeIndex::<u32>::new(self.inv[e] as usize)].to_string(),

Diff for: ‎kmer_lookup/src/lib.rs

+1-1
Original file line numberDiff line numberDiff line change
@@ -152,7 +152,7 @@ pub fn make_kmer_lookup_oriented_single(dv: &[DnaString], x: &mut Vec<(Kmer20, i
152152
if s.len() < K {
153153
starts.push(z);
154154
} else {
155-
let y: usize = z + s.len() as usize - K + 1;
155+
let y: usize = z + s.len() - K + 1;
156156
starts.push(y);
157157
}
158158
}

Diff for: ‎mirror_sparse_matrix/src/lib.rs

+1-1
Original file line numberDiff line numberDiff line change
@@ -598,7 +598,7 @@ mod tests {
598598
} else {
599599
10000 * i + j
600600
};
601-
y.push((col as i32, (i * i * j) as i32));
601+
y.push((col, (i * i * j)));
602602
}
603603
x.push(y);
604604
}

Diff for: ‎pretty_trace/src/lib.rs

+1-1
Original file line numberDiff line numberDiff line change
@@ -442,7 +442,7 @@ impl PrettyTrace {
442442
443443
pub fn on(&mut self) {
444444
let fd = if self.fd.is_some() {
445-
self.fd.unwrap() as i32
445+
self.fd.unwrap()
446446
} else {
447447
-1_i32
448448
};

Diff for: ‎stats_utils/src/lib.rs

+1-1
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,7 @@ pub fn n90(v: &[i32]) -> i32 {
4949
vs.sort_unstable();
5050
for i in 0..vs.len() {
5151
part += i64::from(vs[i]);
52-
if 10 * (part as i64) == 9 * sum as i64 && i < vs.len() - 1 {
52+
if 10 * part == 9 * sum && i < vs.len() - 1 {
5353
return (vs[i] + vs[i + 1]) / 2;
5454
}
5555
if part as f64 / sum as f64 >= 0.9_f64 {

Diff for: ‎vdj_ann/src/annotate.rs

+14-16
Original file line numberDiff line numberDiff line change
@@ -264,15 +264,15 @@ pub fn annotate_seq_core(
264264
if b.len() < K {
265265
return;
266266
}
267-
for l in 0..(b.len() - K + 1) as usize {
267+
for l in 0..(b.len() - K + 1) {
268268
let x: Kmer12 = b.get_kmer(l);
269269
let low = lower_bound1_3(rkmers_plus, &x) as usize;
270270
for r in low..rkmers_plus.len() {
271271
if rkmers_plus[r].0 != x {
272272
break;
273273
}
274-
let t = rkmers_plus[r as usize].1 as usize;
275-
let p = rkmers_plus[r as usize].2 as usize;
274+
let t = rkmers_plus[r].1 as usize;
275+
let p = rkmers_plus[r].2 as usize;
276276
if l > 0 && p > 0 && b_seq[l - 1] == refs[t].get(p - 1) {
277277
continue;
278278
}
@@ -593,9 +593,7 @@ pub fn annotate_seq_core(
593593
let mut mis = semi[i].4.clone();
594594
let mut mis_count = 0;
595595
while l + len < b_seq.len() as i32 && l + len + off < refs[t as usize].len() as i32 {
596-
if b_seq[(l + len as i32) as usize]
597-
!= refs[t as usize].get((l + off + len as i32) as usize)
598-
{
596+
if b_seq[(l + len) as usize] != refs[t as usize].get((l + off + len) as usize) {
599597
mis.push(l + len);
600598
mis_count += 1;
601599
}
@@ -1129,8 +1127,8 @@ pub fn annotate_seq_core(
11291127
continue;
11301128
}
11311129
let (p1, p2) = (annx[i1].3, annx[i2].3);
1132-
let (start1, stop1) = (l1 as usize, (l2 + len2) as usize); // extent on contig
1133-
let (start2, stop2) = (p1 as usize, (p2 as usize + len2) as usize); // extent on ref
1130+
let (start1, stop1) = (l1, (l2 + len2)); // extent on contig
1131+
let (start2, stop2) = (p1 as usize, (p2 as usize + len2)); // extent on ref
11341132
if !(start1 < stop1 && start2 < stop2) {
11351133
continue;
11361134
}
@@ -1169,12 +1167,12 @@ pub fn annotate_seq_core(
11691167
let mut mis2 = Vec::<i32>::new();
11701168
for p in start1..ipos {
11711169
if b_seq[p as usize] != refs[t].get((p + off1) as usize) {
1172-
mis1.push(p as i32);
1170+
mis1.push(p);
11731171
}
11741172
}
11751173
for p in ipos + ins..stop1 {
11761174
if b_seq[p as usize] != refs[t].get((p + off2) as usize) {
1177-
mis2.push(p as i32);
1175+
mis2.push(p);
11781176
}
11791177
}
11801178
let mis = (mis1.len() + mis2.len()) as i32;
@@ -1406,7 +1404,7 @@ pub fn annotate_seq_core(
14061404
let mut locs = Vec::<usize>::new();
14071405
let mut rstarts = Vec::<usize>::new();
14081406
for k in i..j {
1409-
locs.push(combo[k].2 as usize);
1407+
locs.push(combo[k].2);
14101408
let a = &annx[combo[k].2];
14111409
rstarts.push(a.3 as usize);
14121410
cov.push((a.0 as usize, (a.0 + a.1) as usize));
@@ -1582,13 +1580,13 @@ pub fn annotate_seq_core(
15821580

15831581
let (mut zstop1, mut zstop2) = (0, 0);
15841582
for l in 0..data[i1].2.len() {
1585-
let t = annx[data[i1].2[l] as usize].2 as usize;
1583+
let t = annx[data[i1].2[l]].2 as usize;
15861584
if refdata.is_v(t) && (data[i1].3[l] == 0 || data[i1].0[l].0 == 0) {
15871585
zstop1 = max(zstop1, data[i1].0[l].1);
15881586
}
15891587
}
15901588
for l in 0..data[i2].2.len() {
1591-
let t = annx[data[i2].2[l] as usize].2 as usize;
1589+
let t = annx[data[i2].2[l]].2 as usize;
15921590
if refdata.is_v(t) && (data[i2].3[l] == 0 || data[i2].0[l].0 == 0) {
15931591
zstop2 = max(zstop2, data[i2].0[l].1);
15941592
}
@@ -1640,7 +1638,7 @@ pub fn annotate_seq_core(
16401638
if verbose {
16411639
fwriteln!(log, "\nCOMPARING");
16421640
for l in 0..data[i1].2.len() {
1643-
let t = annx[data[i1].2[l] as usize].2 as usize;
1641+
let t = annx[data[i1].2[l]].2 as usize;
16441642
let cov = &data[i1].0[l];
16451643
let mis = data[i1].1;
16461644
fwriteln!(
@@ -1654,7 +1652,7 @@ pub fn annotate_seq_core(
16541652
}
16551653
fwriteln!(log, "TO");
16561654
for l in 0..data[i2].2.len() {
1657-
let t = annx[data[i2].2[l] as usize].2 as usize;
1655+
let t = annx[data[i2].2[l]].2 as usize;
16581656
let cov = &data[i2].0[l];
16591657
let mis = data[i2].1;
16601658
fwriteln!(
@@ -2232,7 +2230,7 @@ pub fn annotate_seq_core(
22322230
let mut vs = Vec::<(usize, usize)>::new();
22332231
for i in 0..annx.len() {
22342232
let t = annx[i].2 as usize;
2235-
if !rheaders[t as usize].contains("V-REGION") {
2233+
if !rheaders[t].contains("V-REGION") {
22362234
continue;
22372235
}
22382236
vs.push((t, i));

Diff for: ‎vdj_ann/src/transcript.rs

+7-7
Original file line numberDiff line numberDiff line change
@@ -42,9 +42,9 @@ pub fn is_valid(
4242
let mut igh = false;
4343
for j in 0..ann.len() {
4444
let l = ann[j].0 as usize;
45-
let len = ann[j as usize].1 as usize;
46-
let t = ann[j as usize].2 as usize;
47-
let p = ann[j as usize].3 as usize;
45+
let len = ann[j].1 as usize;
46+
let t = ann[j].2 as usize;
47+
let p = ann[j].3 as usize;
4848
if rheaders[t].contains("IGH") {
4949
igh = true;
5050
}
@@ -212,9 +212,9 @@ pub fn junction_seq(
212212
let mut jstops = Vec::<i32>::new();
213213
for j in 0..ann.len() {
214214
let l = ann[j].0 as usize;
215-
let len = ann[j as usize].1 as usize;
216-
let t = ann[j as usize].2 as usize;
217-
let p = ann[j as usize].3 as usize;
215+
let len = ann[j].1 as usize;
216+
let t = ann[j].2 as usize;
217+
let p = ann[j].3 as usize;
218218
if (rheaders[t].contains("TRAJ")
219219
|| rheaders[t].contains("IGHJ")
220220
|| rheaders[t].contains("TRBJ")
@@ -304,7 +304,7 @@ pub fn junction_supp_core(
304304
if kmers_plus[m].0 != z {
305305
break;
306306
}
307-
let p = kmers_plus[m as usize].2 as usize;
307+
let p = kmers_plus[m].2 as usize;
308308
if j > 0 && p > 0 && b.get(j - 1) == jseq.get(p - 1) {
309309
continue;
310310
}

Diff for: ‎vector_utils/src/lib.rs

+4-4
Original file line numberDiff line numberDiff line change
@@ -253,7 +253,7 @@ pub fn bin_position<T: Ord + ?Sized>(x: &[impl Borrow<T>], d: &T) -> i32 {
253253
}
254254

255255
pub fn bin_position1_2<S: Ord + ?Sized, T: Ord>(x: &[(impl Borrow<S>, T)], d: &S) -> i32 {
256-
match x.binary_search_by_key(&d, |&(ref a, ref _b)| a.borrow()) {
256+
match x.binary_search_by_key(&d, |(a, _b)| a.borrow()) {
257257
Ok(p) => p as i32,
258258
Err(_e) => -1,
259259
}
@@ -263,7 +263,7 @@ pub fn bin_position1_3<S: Ord + ?Sized, T: Ord, U: Ord>(
263263
x: &[(impl Borrow<S>, T, U)],
264264
d: &S,
265265
) -> i32 {
266-
match x.binary_search_by_key(&d, |&(ref a, ref _b, ref _c)| a.borrow()) {
266+
match x.binary_search_by_key(&d, |(a, _b, _c)| a.borrow()) {
267267
Ok(p) => p as i32,
268268
Err(_e) => -1,
269269
}
@@ -273,7 +273,7 @@ pub fn bin_position1_4<S: Ord + ?Sized, T: Ord, U: Ord, V: Ord>(
273273
x: &[(impl Borrow<S>, T, U, V)],
274274
d: &S,
275275
) -> i32 {
276-
match x.binary_search_by_key(&d, |&(ref a, ref _b, ref _c, ref _d)| a.borrow()) {
276+
match x.binary_search_by_key(&d, |(a, _b, _c, _d)| a.borrow()) {
277277
Ok(p) => p as i32,
278278
Err(_e) => -1,
279279
}
@@ -283,7 +283,7 @@ pub fn bin_position1_5<S: Ord + ?Sized, T: Ord, U: Ord, V: Ord, W: Ord>(
283283
x: &[(impl Borrow<S>, T, U, V, W)],
284284
d: &S,
285285
) -> i32 {
286-
match x.binary_search_by_key(&d, |&(ref a, ref _b, ref _c, ref _d, ref _e)| a.borrow()) {
286+
match x.binary_search_by_key(&d, |(a, _b, _c, _d, _e)| a.borrow()) {
287287
Ok(p) => p as i32,
288288
Err(_e) => -1,
289289
}

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