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fix: memory efficient poa bug fix #552

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fix: memory efficient poa bug fix #552

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bbde79f
fixes set and get of start cell
lorewar2 Sep 13, 2023
e586b24
Merge branch 'master' into poa_small_fix
johanneskoester Oct 18, 2023
60e6bf3
fix row end set and get
lorewar2 Nov 14, 2023
fab758d
Merge branch 'master' into poa_small_fix
lorewar2 Nov 14, 2023
5934990
out of band fix
lorewar2 Nov 20, 2023
157f9c0
Merge branch 'poa_small_fix' of https://github.com/lorewar2/rust-bio …
lorewar2 Nov 20, 2023
8cadb79
0 len rows skip
lorewar2 Nov 21, 2023
ae7f3b3
Merge branch 'master' into poa_small_fix
lorewar2 Jan 11, 2024
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12 changes: 6 additions & 6 deletions src/alignment/poa.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,7 @@ impl Traceback {
/// * `n` - the length of the query sequence
fn with_capacity(m: usize, n: usize) -> Self {
// each row of matrix contain start end position and vec of traceback cells
let matrix: Vec<(Vec<TracebackCell>, usize, usize)> = vec![(vec![], 0, n); m + 1];
let matrix: Vec<(Vec<TracebackCell>, usize, usize)> = vec![(vec![], 0, n + 1); m + 1];
Traceback {
rows: m,
cols: n,
Expand Down Expand Up @@ -268,15 +268,15 @@ impl Traceback {

fn set(&mut self, i: usize, j: usize, cell: TracebackCell) {
// set the matrix cell if in band range
if !(self.matrix[i].1 > j || self.matrix[i].2 < j) {
if !(self.matrix[i].1 > j || self.matrix[i].2 <= j) {
let real_position = j - self.matrix[i].1;
self.matrix[i].0[real_position] = cell;
}
}

fn get(&self, i: usize, j: usize) -> &TracebackCell {
// get the matrix cell if in band range else return the appropriate values
if !(self.matrix[i].1 > j || self.matrix[i].2 < j) {
if !(self.matrix[i].1 > j || self.matrix[i].2 <= j) && (self.matrix[i].0.len() > 0) {
let real_position = j - self.matrix[i].1;
return &self.matrix[i].0[real_position];
}
Expand All @@ -288,7 +288,7 @@ impl Traceback {
};
}
// infront of the band
else if j > self.matrix[i].2 {
else if j >= self.matrix[i].2 {
return &TracebackCell {
score: MIN_SCORE,
op: AlignmentOperation::Ins(None),
Expand Down Expand Up @@ -507,7 +507,7 @@ impl<F: MatchFunc> Poa<F> {
// iterate over the predecessors of this node
let prevs: Vec<NodeIndex<usize>> =
self.graph.neighbors_directed(node, Incoming).collect();
traceback.new_row(i, n + 1, self.scoring.gap_open, 0, n);
traceback.new_row(i, n + 1, self.scoring.gap_open, 0, n + 1);
// query base and its index in the DAG (traceback matrix rows)
for (query_index, query_base) in query.iter().enumerate() {
let j = query_index + 1; // 0 index is initialized so we start at 1
Expand Down Expand Up @@ -600,7 +600,7 @@ impl<F: MatchFunc> Poa<F> {
max_scoring_j - bandwidth
};
let end = max_scoring_j + bandwidth;
traceback.new_row(i, (end - start) + 1, self.scoring.gap_open, start, end);
traceback.new_row(i, (end - start) + 1, self.scoring.gap_open, start, end + 1);
for (query_index, query_base) in query.iter().enumerate().skip(start) {
let j = query_index + 1; // 0 index is initialized so we start at 1
if j > end {
Expand Down