Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feat: update to bio-types 1.0 #524

Merged
merged 2 commits into from
Jun 14, 2023
Merged

feat: update to bio-types 1.0 #524

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
8157330
Update Cargo.toml
johanneskoester Jun 6, 2023
d1f21c4
add missing parameter
johanneskoester Jun 13, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
2 changes: 1 addition & 1 deletion Cargo.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ regex = { version = "1.3", default-features = false, features = ["std", "perf"]
multimap = ">=0.6, <0.9"
fxhash = "0.2"
statrs = ">= 0.11, < 0.17"
bio-types = ">=0.11.0"
bio-types = ">=1.0.0"
pest = { version = "2", optional = true }
pest_derive = { version = "2", optional = true }
strum = ">= 0.16, < 0.25"
Expand Down
18 changes: 9 additions & 9 deletions src/alignment/pairwise/banded.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@
//! let y = b"AAAAACGTACGTACGTGTGCATCATCATGTGCGTATCATAGATAGATGTAGATGATCCACAGTAAAA";
//! let mut aligner = Aligner::with_capacity_and_scoring(x.len(), y.len(), scoring, k, w);
//! let alignment = aligner.custom(x, y);
//! println!("{}", alignment.pretty(x, y));
//! println!("{}", alignment.pretty(x, y, 80));
//! assert_eq!(alignment.score, 49);
//! let mut correct_ops = Vec::new();
//! correct_ops.push(Yclip(4));
Expand Down Expand Up @@ -1262,7 +1262,7 @@
// Band to lower right corner
let rows = self.rows as u32;
let cols = self.cols as u32;
self.add_gap((r as u32, c as u32), (rows as u32, cols as u32), w);

Check warning on line 1265 in src/alignment/pairwise/banded.rs

View workflow job for this annotation

GitHub Actions / clippy

casting to the same type is unnecessary (`u32` -> `u32`) 

warning: casting to the same type is unnecessary (`u32` -> `u32`)
    --> src/alignment/pairwise/banded.rs:1265:70
     |
1265 |                     self.add_gap((r as u32, c as u32), (rows as u32, cols as u32), w);
     |                                                                      ^^^^^^^^^^^ help: try: `cols`
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast

Check warning on line 1265 in src/alignment/pairwise/banded.rs

View workflow job for this annotation

GitHub Actions / clippy

casting to the same type is unnecessary (`u32` -> `u32`) 

warning: casting to the same type is unnecessary (`u32` -> `u32`)
    --> src/alignment/pairwise/banded.rs:1265:57
     |
1265 |                     self.add_gap((r as u32, c as u32), (rows as u32, cols as u32), w);
     |                                                         ^^^^^^^^^^^ help: try: `rows`
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
     = note: `#[warn(clippy::unnecessary_cast)]` on by default
}
}
}
Expand Down Expand Up @@ -1795,7 +1795,7 @@
let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
let alignment = aligner.global(x, y);

println!("aln:\n{}", alignment.pretty(x, y));
println!("aln:\n{}", alignment.pretty(x, y, 80));
assert_eq!(
alignment.operations,
[Match, Match, Match, Ins, Ins, Ins, Match, Match, Match]
Expand All @@ -1810,7 +1810,7 @@
let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
let alignment = aligner.local(x, y);

println!("aln:\n{}", alignment.pretty(x, y));
println!("aln:\n{}", alignment.pretty(x, y, 80));
assert_eq!(alignment.x_aln_len(), 0);
assert_eq!(alignment.y_aln_len(), 0);
}
Expand All @@ -1823,7 +1823,7 @@
let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
let alignment = aligner.global(x, y);

println!("aln:\n{}", alignment.pretty(x, y));
println!("aln:\n{}", alignment.pretty(x, y, 80));

let mut correct = Vec::new();
correct.extend(repeat(Match).take(11));
Expand Down Expand Up @@ -1867,7 +1867,7 @@
let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
let alignment = aligner.global(x, y);

println!("\naln:\n{}", alignment.pretty(x, y));
println!("\naln:\n{}", alignment.pretty(x, y, 80));
assert_eq!(alignment.ystart, 0);
assert_eq!(alignment.xstart, 0);
assert_eq!(
Expand Down Expand Up @@ -1969,7 +1969,7 @@
let score = |a: u8, b: u8| if a == b { 1i32 } else { -1i32 };
let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
let alignment = aligner.global(x, y);
println!("\naln:\n{}", alignment.pretty(x, y));
println!("\naln:\n{}", alignment.pretty(x, y, 80));

assert_eq!(alignment.ystart, 0);
assert_eq!(alignment.xstart, 0);
Expand All @@ -1993,7 +1993,7 @@
let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
let alignment = aligner.global(x, y);

println!("\naln:\n{}", alignment.pretty(x, y));
println!("\naln:\n{}", alignment.pretty(x, y, 80));

println!("score:{}", alignment.score);
assert_eq!(alignment.score, -9);
Expand All @@ -2015,7 +2015,7 @@
let score = |a: u8, b: u8| if a == b { 1i32 } else { -1i32 };
let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
let alignment = aligner.global(x, y);
println!("\naln:\n{}", alignment.pretty(x, y));
println!("\naln:\n{}", alignment.pretty(x, y, 80));

assert_eq!(alignment.ystart, 0);
assert_eq!(alignment.xstart, 0);
Expand Down Expand Up @@ -2169,7 +2169,7 @@
let mut aligner = banded::Aligner::with_scoring(scoring, 10, 10);
let alignment = aligner.custom(x, y);

println!("{}", alignment.pretty(x, y));
println!("{}", alignment.pretty(x, y, 80));
assert_eq!(alignment.score, 7);
}

Expand Down
16 changes: 8 additions & 8 deletions src/alignment/pairwise/mod.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,7 @@
//! let y = b"AAAAACGTACGTACGTAAAA";
//! let mut aligner = Aligner::with_capacity_and_scoring(x.len(), y.len(), scoring);
//! let alignment = aligner.custom(x, y);
//! println!("{}", alignment.pretty(x, y));
//! println!("{}", alignment.pretty(x, y, 80));
//! assert_eq!(alignment.score, 2);
//! assert_eq!(
//! alignment.operations,
Expand Down Expand Up @@ -1231,7 +1231,7 @@ mod tests {
let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, score);
let alignment = aligner.global(x, y);

println!("aln:\n{}", alignment.pretty(x, y));
println!("aln:\n{}", alignment.pretty(x, y, 80));
assert_eq!(
alignment.operations,
[Match, Match, Match, Ins, Ins, Ins, Match, Match, Match]
Expand All @@ -1246,7 +1246,7 @@ mod tests {
let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, score);
let alignment = aligner.global(x, y);

println!("aln:\n{}", alignment.pretty(x, y));
println!("aln:\n{}", alignment.pretty(x, y, 80));

let mut correct = Vec::new();
correct.extend(repeat(Match).take(11));
Expand Down Expand Up @@ -1290,7 +1290,7 @@ mod tests {
let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, score);
let alignment = aligner.global(x, y);

println!("\naln:\n{}", alignment.pretty(x, y));
println!("\naln:\n{}", alignment.pretty(x, y, 80));
assert_eq!(alignment.ystart, 0);
assert_eq!(alignment.xstart, 0);
assert_eq!(
Expand Down Expand Up @@ -1409,7 +1409,7 @@ mod tests {
let score = |a: u8, b: u8| if a == b { 1i32 } else { -1i32 };
let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, &score);
let alignment = aligner.global(x, y);
println!("\naln:\n{}", alignment.pretty(x, y));
println!("\naln:\n{}", alignment.pretty(x, y, 80));

assert_eq!(alignment.ystart, 0);
assert_eq!(alignment.xstart, 0);
Expand All @@ -1433,7 +1433,7 @@ mod tests {
let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, &score);
let alignment = aligner.global(x, y);

println!("\naln:\n{}", alignment.pretty(x, y));
println!("\naln:\n{}", alignment.pretty(x, y, 80));

println!("score:{}", alignment.score);
assert_eq!(alignment.score, -9);
Expand All @@ -1455,7 +1455,7 @@ mod tests {
let score = |a: u8, b: u8| if a == b { 1i32 } else { -1i32 };
let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, &score);
let alignment = aligner.global(x, y);
println!("\naln:\n{}", alignment.pretty(x, y));
println!("\naln:\n{}", alignment.pretty(x, y, 80));

assert_eq!(alignment.ystart, 0);
assert_eq!(alignment.xstart, 0);
Expand Down Expand Up @@ -1633,7 +1633,7 @@ mod tests {
let mut aligner = Aligner::with_scoring(scoring);
let alignment = aligner.custom(x, y);

println!("{}", alignment.pretty(x, y));
println!("{}", alignment.pretty(x, y, 80));
assert_eq!(alignment.score, 7);
}

Expand Down
4 changes: 2 additions & 2 deletions src/pattern_matching/myers/mod.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@
//! let mut matches = myers.find_all(text, 3);
//! while matches.next_alignment(&mut aln) {
//! //println!("Hit fond in range: {}..{} (distance: {})", aln.ystart, aln.yend, aln.score);
//! //println!("{}", aln.pretty(pattern, text));
//! //println!("{}", aln.pretty(pattern, text, 80));
//! }
//! # }
//! ```
Expand Down Expand Up @@ -192,7 +192,7 @@
//! "Best alignment at {}..{} (distance: {})",
//! aln.ystart, aln.yend, aln.score
//! );
//! println!("{}", aln.pretty(pattern, text));
//! println!("{}", aln.pretty(pattern, text, 80));
//! # }
//! ```
//!
Expand Down