Skip to content

replace manual vector initialization #19

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

Open
bmesuere wants to merge 2 commits into
base: benchmark/1
Choose a base branch
from
Open

replace manual vector initialization #19

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
08124bd
replace manual vector initialization
bmesuere Feb 2, 2026
82c98e4
skip Viterbi for sequences shorter than 3 nucleotides
bmesuere Feb 2, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion src/bin/FragGeneScanRs.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -245,7 +245,7 @@ fn run<R: Read + Send, W: WritingBuffer + Send>(
.map(u8::to_ascii_uppercase)
.map(Nuc::from)
.collect();
let read_prediction = if nseq.is_empty() {
let read_prediction = if nseq.len() < 3 {
gene::ReadPrediction::new(head)
} else {
viterbi(&global, &locals, head, nseq, whole_genome)
Expand Down
10 changes: 3 additions & 7 deletions src/viterbi.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,15 +27,11 @@ pub fn forward(
Vec<[f64; hmm::State::COUNT]>,
Vec<[Option<hmm::State>; hmm::State::COUNT]>,
) {
let mut alpha: Vec<[f64; hmm::State::COUNT]> = Vec::with_capacity(seq.len());
let mut path: Vec<[Option<hmm::State>; hmm::State::COUNT]> = Vec::with_capacity(seq.len());
let mut alpha: Vec<[f64; hmm::State::COUNT]> = vec![[0.0; hmm::State::COUNT]; seq.len()];
let mut path: Vec<[Option<hmm::State>; hmm::State::COUNT]> =
vec![[Some(hmm::State::S); hmm::State::COUNT]; seq.len()];
Comment on lines +30 to +32
Copy link

Copilot AI Feb 2, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

forward() allocates alpha/path using seq.len(), but the function later unconditionally indexes alpha[0] and seq[0..=2] (and writes to alpha[1]/alpha[2]). Since the caller currently only guards is_empty(), inputs with length 1–2 will panic. Consider adding an early return/guard for seq.len() < 3 (either here or in viterbi()/caller) so short records are handled safely.

Copilot uses AI. Check for mistakes.
Copy link
Member Author

@bmesuere bmesuere Feb 2, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is a valid comment, but was also valid for the original code. I fixed it at the caller side in FragGeneScanRs.rs.

let mut temp_i: [usize; hmm::PERIOD] = [0; hmm::PERIOD];
let mut temp_i_1: [usize; hmm::PERIOD] = [0; hmm::PERIOD];

for _ in 0..seq.len() {
alpha.push([0.0; hmm::State::COUNT]);
path.push([Some(hmm::State::S); hmm::State::COUNT]);
}
alpha[0].copy_from_slice(&global.pi);
for i in &mut alpha[0] {
*i *= -1.0
Expand Down