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Switch genome name lookup to hashmap #40

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Switch genome name lookup to hashmap #40

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14 changes: 5 additions & 9 deletions src/skani.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ use skani::params::*;
use skani::screen;

use concurrent_queue::ConcurrentQueue;
use std::collections::HashMap;

pub struct SkaniPreclusterer {
pub threshold: f32,
Expand Down Expand Up @@ -44,6 +45,7 @@ fn precluster_skani(
.collect::<Vec<String>>();
// Note that sketches is now shuffled!
let sketches = &file_io::fastx_to_sketches(&fasta_strings, &sketch_params, true);
let genome_indices: HashMap<_, _> = genome_fasta_paths.into_iter().enumerate().map(|(index, element)| (element, index)).collect();

// Right now implemented by parallel collection into a queue, and then
// reprocessed into a BTreeMap. Could potentially be made more efficient by
Expand Down Expand Up @@ -78,14 +80,8 @@ fn precluster_skani(
let query_name = sketches[j].file_name.clone();
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@wwood I tried using String::from(ref_sketch.file_name) and String::from(ref_sketch.file_name.clone()) but get the same error. Did you mean somewhere else?


debug!("Pushing ANI result for {} and {}", ref_name, query_name);
let ref_index = genome_fasta_paths
.iter()
.position(|&r| r == ref_name)
.unwrap();
let query_index = genome_fasta_paths
.iter()
.position(|&r| r == query_name)
.unwrap();
let ref_index = genome_indices.get(&ref_name).unwrap();
let query_index = genome_indices.get(&query_name).unwrap();
if ani >= threshold {
queue
.push((ref_index, query_index, ani))
Expand All @@ -98,7 +94,7 @@ fn precluster_skani(

let mut to_return = SortedPairGenomeDistanceCache::new();
while let Ok((i, j, ani)) = queue.pop() {
to_return.insert((i, j), Some(ani));
to_return.insert((*i, *j), Some(ani));
}
debug!("Finished skani.");

Expand Down
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