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fix: pretty print with suffix xclip or yclip #63

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fix: pretty print with suffix xclip or yclip #63

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21 changes: 19 additions & 2 deletions src/alignment.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -49,11 +49,11 @@
Custom,
}

impl Default for AlignmentMode {
fn default() -> Self {
AlignmentMode::Global
}
}

Check warning on line 56 in src/alignment.rs

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GitHub Actions / clippy

this `impl` can be derived 

warning: this `impl` can be derived
  --> src/alignment.rs:52:1
   |
52 | / impl Default for AlignmentMode {
53 | |     fn default() -> Self {
54 | |         AlignmentMode::Global
55 | |     }
56 | | }
   | |_^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#derivable_impls
   = note: `#[warn(clippy::derivable_impls)]` on by default
   = help: remove the manual implementation...
help: ...and instead derive it...
   |
45 + #[derive(Default)]
46 | pub enum AlignmentMode {
   |
help: ...and mark the default variant
   |
48 ~     #[default]
49 ~     Global,
   |

/// We consider alignment between two sequences x and y. x is the query or read sequence
/// and y is the reference or template sequence. An alignment, consisting of a score,
Expand Down Expand Up @@ -259,7 +259,7 @@
y_pretty.push('-');
}
AlignmentOperation::Xclip(len) => {
for k in x.iter().take(len) {
for k in x.iter().skip(x_i).take(len) {
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Are you sure this doesn't break non-Custom Alignments? Or maybe to be clearer, is there either (i) a test case that also covers this for for some non-custom Alignment? I could imagine, that the special casing further up is the actual problem? But you dug into this code in more detail, so are probably more confident in answering those question.

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@dcroote Will you have time to have another look here? Otherwise I would probably move ahead with release 1.0.1 at #62 for now...

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Sorry for the delay- I'll need more time to flesh out the test cases so feel free to move ahead with the release

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Just a quick ping to see if there is any planned activity, here. If so, feel free to update the branch, first.

x_pretty.push_str(&format!("{}", String::from_utf8_lossy(&[*k])));
x_i += 1;

Expand All @@ -269,7 +269,7 @@
}
}
AlignmentOperation::Yclip(len) => {
for k in y.iter().take(len) {
for k in y.iter().skip(y_i).take(len) {
y_pretty.push_str(&format!("{}", String::from_utf8_lossy(&[*k])));
y_i += 1;

Expand Down Expand Up @@ -537,4 +537,21 @@
]
)
}

#[test]
fn test_pretty_suffix_xclip_or_yclip() {
let alignment = Alignment {
score: -7,
ystart: 1,
xstart: 0,
yend: 4,
xend: 3,
ylen: 4,
xlen: 4,
operations: vec![Yclip(1), Match, Match, Match, Xclip(1)],
mode: AlignmentMode::Custom,
};
let pretty = concat!(" TCGC\n ||| \nATCG \n\n\n");
assert_eq!(alignment.pretty(b"TCGC", b"ATCG", 100), pretty);
}
}
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