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

Cache cigars #48

Draft
wants to merge 2 commits into
base: main
Choose a base branch
from
Draft

Cache cigars #48

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4c15d72
Small perf improvement for parse_cigar_delta
bkille Feb 3, 2025
7c1eec9
Cache cigars
bkille Feb 5, 2025
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
66 changes: 40 additions & 26 deletions src/impg.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ use crate::seqidx::SequenceIndex;
use serde::{Serialize, Deserialize};
use std::io::{Read, SeekFrom, Seek};
use std::fs::File;
use std::cell::RefCell;
use rayon::prelude::*;
use noodles::bgzf;
use regex::Regex;
Expand Down Expand Up @@ -86,23 +87,33 @@ pub struct QueryMetadata {
}

impl QueryMetadata {
fn get_cigar_ops(&self, paf_file: &String, paf_gzi_index: Option<&bgzf::gzi::Index>) -> Vec<CigarOp> {
// Allocate space for cigar
let mut cigar_buffer = vec![0; self.cigar_bytes];

// Get reader and seek start of cigar str
if [".gz", ".bgz"].iter().any(|e| paf_file.ends_with(e)) {
let mut reader = bgzf::Reader::new(File::open(paf_file).unwrap());
reader.seek_by_uncompressed_position(paf_gzi_index.unwrap(), self.cigar_offset).unwrap();
reader.read_exact(&mut cigar_buffer).unwrap();
} else {
let mut reader = File::open(paf_file).unwrap();
reader.seek(SeekFrom::Start(self.cigar_offset)).unwrap();
reader.read_exact(&mut cigar_buffer).unwrap();
};
fn fetch_cigar_ops(
&self,
paf_file: &String,
paf_gzi_index: Option<&bgzf::gzi::Index>,
offset_to_cigar: &mut FxHashMap::<u64, Vec<CigarOp>>
) {

let cigar_str: &str = std::str::from_utf8(&cigar_buffer).unwrap();
parse_cigar_to_delta(cigar_str).ok().unwrap_or_default()
if !offset_to_cigar.contains_key(&self.cigar_offset)
{
if offset_to_cigar.len() > 1000 { offset_to_cigar.clear(); }
// Allocate space for cigar
let mut cigar_buffer = vec![0; self.cigar_bytes];

// Get reader and seek start of cigar str
if [".gz", ".bgz"].iter().any(|e| paf_file.ends_with(e)) {
let mut reader = bgzf::Reader::new(File::open(paf_file).unwrap());
reader.seek_by_uncompressed_position(paf_gzi_index.unwrap(), self.cigar_offset).unwrap();
reader.read_exact(&mut cigar_buffer).unwrap();
} else {
let mut reader = File::open(paf_file).unwrap();
reader.seek(SeekFrom::Start(self.cigar_offset)).unwrap();
reader.read_exact(&mut cigar_buffer).unwrap();
};

let cigar_str: &str = std::str::from_utf8(&cigar_buffer).unwrap();
offset_to_cigar.insert(self.cigar_offset, parse_cigar_to_delta(cigar_str).ok().unwrap_or_default());
}
}
}

Expand Down Expand Up @@ -240,12 +251,13 @@ impl SortedRanges {
}
}

#[derive(Clone)]
//#[derive(Clone)]
pub struct Impg {
pub trees: TreeMap,
pub seq_index: SequenceIndex,
pub paf_file: String,
pub paf_gzi_index: Option<bgzf::gzi::Index>,
pub offset_to_cigar: RefCell<FxHashMap<u64, Vec<CigarOp>>>,
}

impl Impg {
Expand Down Expand Up @@ -300,7 +312,8 @@ impl Impg {
(target_id, BasicCOITree::new(interval_nodes.as_slice()))
}).collect();

Ok(Self { trees, seq_index, paf_file: paf_file.to_string(), paf_gzi_index })
let offset_to_cigar = RefCell::new(FxHashMap::default());
Ok(Self { trees, seq_index, paf_file: paf_file.to_string(), paf_gzi_index, offset_to_cigar })
}

pub fn to_serializable(&self) -> SerializableImpg {
Expand Down Expand Up @@ -331,7 +344,8 @@ impl Impg {
}).collect::<Vec<_>>().as_slice());
(target_id, tree)
}).collect();
Self { trees, seq_index, paf_file: paf_file.to_string(), paf_gzi_index }
let offset_to_cigar = RefCell::new(FxHashMap::default());
Self { trees, seq_index, paf_file: paf_file.to_string(), paf_gzi_index, offset_to_cigar }
}

pub fn query(
Expand Down Expand Up @@ -361,10 +375,11 @@ impl Impg {
if let Some(tree) = self.trees.get(&target_id) {
tree.query(range_start, range_end, |interval| {
let metadata = &interval.metadata;
metadata.fetch_cigar_ops(&self.paf_file, self.paf_gzi_index.as_ref(), &mut *self.offset_to_cigar.borrow_mut());
let result = project_target_range_through_alignment(
(range_start, range_end),
(metadata.target_start, metadata.target_end, metadata.query_start, metadata.query_end, metadata.strand),
&metadata.get_cigar_ops(&self.paf_file, self.paf_gzi_index.as_ref()),
&self.offset_to_cigar.borrow()[&metadata.cigar_offset],
true
);
if let Some((adjusted_query_start, adjusted_query_end, adjusted_cigar, adjusted_target_start, adjusted_target_end)) = result {
Expand Down Expand Up @@ -450,10 +465,11 @@ impl Impg {
if let Some(tree) = self.trees.get(&current_target_id) {
tree.query(current_target_start, current_target_end, |interval| {
let metadata = &interval.metadata;
metadata.fetch_cigar_ops(&self.paf_file, self.paf_gzi_index.as_ref(), &mut *self.offset_to_cigar.borrow_mut());
let result = project_target_range_through_alignment(
(current_target_start, current_target_end),
(metadata.target_start, metadata.target_end, metadata.query_start, metadata.query_end, metadata.strand),
&metadata.get_cigar_ops(&self.paf_file, self.paf_gzi_index.as_ref()),
&self.offset_to_cigar.borrow()[&metadata.cigar_offset],
store_cigar
);
if let Some((adjusted_query_start, adjusted_query_end, adjusted_cigar, adjusted_target_start, adjusted_target_end)) = result {
Expand Down Expand Up @@ -678,17 +694,15 @@ fn project_target_range_through_alignment(

fn parse_cigar_to_delta(cigar: &str) -> Result<Vec<CigarOp>, ParseErr> {
let mut ops = Vec::new();
let mut num_buf = String::new();
let mut len: i32 = 0;

for c in cigar.chars() {
if c.is_ascii_digit() {
num_buf.push(c);
len = len*10 + (c as i32 - '0' as i32);
} else {
let len = num_buf.parse::<i32>().map_err(|_| ParseErr::InvalidCigarFormat)?;
num_buf.clear(); // Reset the buffer for the next operation
// raise any error from the cigar op parsing
let op = CigarOp::new(len, c);
ops.push(op);
len = 0;
}
}

Expand Down
Loading