refactor: Extract repeated H5 loading code into a couple of small types #810
Annotations
11 warnings
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Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: 10XGenomics/clippy-check@main. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Run clippy:
vector_utils/src/lib.rs#L138
warning: `if` chain can be rewritten with `match`
--> vector_utils/src/lib.rs:138:9
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138 | / if x[i] < y[j] {
139 | | i += 1;
140 | | } else if y[j] < x[i] {
141 | | j += 1;
142 | | } else {
143 | | return true;
144 | | }
| |_________^
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= help: consider rewriting the `if` chain to use `cmp` and `match`
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#comparison_chain
= note: `#[warn(clippy::comparison_chain)]` on by default
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Run clippy:
vector_utils/src/lib.rs#L158
warning: `if` chain can be rewritten with `match`
--> vector_utils/src/lib.rs:158:9
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158 | / if x[i] < y[j] {
159 | | i += 1;
160 | | } else if y[j] < x[i] {
161 | | j += 1;
... |
165 | | j += 1;
166 | | }
| |_________^
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= help: consider rewriting the `if` chain to use `cmp` and `match`
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#comparison_chain
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Run clippy:
vector_utils/src/lib.rs#L177
warning: `if` chain can be rewritten with `match`
--> vector_utils/src/lib.rs:177:9
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177 | / if x[ix] < y[iy] {
178 | | ix += 1;
179 | | } else if y[iy] < x[ix] {
180 | | iy += 1;
... |
184 | | iy += 1;
185 | | }
| |_________^
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= help: consider rewriting the `if` chain to use `cmp` and `match`
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#comparison_chain
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Run clippy:
tables/src/lib.rs#L255
warning: `if` chain can be rewritten with `match`
--> tables/src/lib.rs:255:17
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255 | / if have > need {
256 | | if debug_print {
257 | | println!(
258 | | "adding {} spaces to right of row {} col {}",
... |
272 | | ext[k - 1] += need - have;
273 | | }
| |_________________^
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= help: consider rewriting the `if` chain to use `cmp` and `match`
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#comparison_chain
= note: `#[warn(clippy::comparison_chain)]` on by default
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Run clippy:
vdj_ann/src/annotate.rs#L295
warning: this function has too many arguments (8/7)
--> vdj_ann/src/annotate.rs:295:1
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295 | / pub fn annotate_seq_core(
296 | | b: &DnaString,
297 | | refdata: &RefData,
298 | | ann: &mut Vec<Annotation>,
... |
303 | | verbose: bool,
304 | | ) {
| |__^
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments
= note: `#[warn(clippy::too_many_arguments)]` on by default
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Run clippy:
dna/src/lib.rs#L129
warning: this function has too many arguments (12/7)
--> dna/src/lib.rs:129:1
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129 | / pub fn get_thermodynamic_parameters_dna(
130 | | dh: &mut Vec<Vec<f64>>,
131 | | ds: &mut Vec<Vec<f64>>,
132 | | dg: &mut Vec<Vec<f64>>,
... |
141 | | dg_symmetry_correction: &mut f64,
142 | | ) {
| |__^
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments
= note: `#[warn(clippy::too_many_arguments)]` on by default
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Run clippy:
vdj_ann/src/annotate.rs#L3199
warning: this function has too many arguments (15/7)
--> vdj_ann/src/annotate.rs:3199:5
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3199 | / pub fn from_annotate_seq(
3200 | | b: &DnaString, // the contig
3201 | | q: &[u8], // qual scores for the contig
3202 | | tigname: &str, // name of the contig
... |
3214 | | jsupp: Option<JunctionSupport>, // num reads, umis supporting junction
3215 | | ) -> ContigAnnotation {
| |_________________________^
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments
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Run clippy:
vdj_ann/src/annotate.rs#L3326
warning: this function has too many arguments (12/7)
--> vdj_ann/src/annotate.rs:3326:5
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3326 | / pub fn from_seq(
3327 | | b: &DnaString, // the contig
3328 | | q: &[u8], // qual scores for the contig
3329 | | tigname: &str, // name of the contig
... |
3338 | | jsupp: Option<JunctionSupport>, // num reads, umis supporting junction
3339 | | ) -> ContigAnnotation {
| |_________________________^
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments
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Run clippy:
vdj_ann_ref/src/lib.rs#L71
warning: this function has too many arguments (8/7)
--> vdj_ann_ref/src/lib.rs:71:1
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71 | / pub fn make_vdj_ref_data(
72 | | refdata: &mut RefData,
73 | | imgt: bool,
74 | | species: &str,
... |
79 | | mouse_supp_ref: &str,
80 | | ) {
| |__^
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments
= note: `#[warn(clippy::too_many_arguments)]` on by default
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Run clippy:
vdj_ann_ref/src/bin/build_vdj_ref.rs#L178
warning: this function has too many arguments (11/7)
--> vdj_ann_ref/src/bin/build_vdj_ref.rs:178:1
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178 | / fn add_gene<R: Write>(
179 | | out: &mut R,
180 | | gene: &str,
181 | | record: &mut usize,
... |
189 | | source: &str,
190 | | ) {
| |__^
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments
= note: `#[warn(clippy::too_many_arguments)]` on by default
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