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Get nerd-sniped and do some micro-optimizations. #41

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Get nerd-sniped and do some micro-optimizations. #41

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104684e
Minor modernizations and optimizations in STAR code.
adam-azarchs Mar 23, 2022
565ee67
Use -fvisibility=hidden and -ffunction-sections.
adam-azarchs Mar 23, 2022
5a4dfb3
Missing edit.
adam-azarchs Mar 23, 2022
104344b
temp log
evolvedmicrobe Sep 2, 2022
9efdf32
Update htslib
evolvedmicrobe Sep 2, 2022
782c6a9
Optimize by default
evolvedmicrobe Sep 3, 2022
a9f26c7
Merge branch 'nd/testing' into azarchs/waste-time
evolvedmicrobe Sep 3, 2022
14353c6
Merge branch 'master' into azarchs/waste-time
adam-azarchs Sep 5, 2022
b34d0ff
Help the vectorizer out.
adam-azarchs Sep 6, 2022
a0f5d95
Rustfmt.
adam-azarchs Sep 6, 2022
205a83d
clippy fix
adam-azarchs Sep 7, 2022
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4 changes: 2 additions & 2 deletions Cargo.lock
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2 changes: 1 addition & 1 deletion Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ include = ["wrapper.h", "src/lib.rs", "LICENSE", "README.md"]
[dependencies]
anyhow = "1"
libc = "0.2"
rust-htslib = { version = "0.38.2", default-features = false, features = ["serde_feature"] }
rust-htslib = { version = "0.39.5", default-features = false, features = ["serde_feature"] }
star-sys = { version = "0.2", path = "star-sys" }

[profile.release]
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14 changes: 13 additions & 1 deletion src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ use std::os::raw::c_char;
use std::os::raw::c_int;
use std::path::Path;
use std::sync::Arc;
use std::time::Instant;

use anyhow::{format_err, Error};
use rust_htslib::bam;
Expand Down Expand Up @@ -253,6 +254,7 @@ impl StarAligner {

/// Aligns a given read and produces BAM records
pub fn align_read(&mut self, name: &[u8], read: &[u8], qual: &[u8]) -> Vec<bam::Record> {
let now = Instant::now();
// STAR will throw an error on empty reads - so just construct an empty record.
if read.len() == 0 {
// Make an unmapped record and return it
Expand All @@ -261,7 +263,17 @@ impl StarAligner {

Self::prepare_fastq(&mut self.fastq1, name, read, qual);
align_read_rust(self.aligner, self.fastq1.as_slice(), &mut self.aln_buf).unwrap();
self.parse_sam_to_records(name)
let record= self.parse_sam_to_records(name);
let new_now = Instant::now();
let (chr, pos, cigar, cigar_ops) = if record.len() > 0 {
let rec = &record[0];
(rec.tid().to_string(), rec.pos().to_string(), format!("{}", rec.cigar()), rec.cigar().len().to_string())
} else {
("NA".to_string(), "NA".to_string(), "NA".to_string(), "NA".to_string())
};
println!("{:?},{:?},{:?},{},{},{},{}", std::str::from_utf8(&read).unwrap(), new_now.duration_since(now), record.len(), chr, pos, cigar, cigar_ops);
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Lots of unnecessary memcpy going on here.

Suggested change
let (chr, pos, cigar, cigar_ops) = if record.len() > 0 {
let rec = &record[0];
(rec.tid().to_string(), rec.pos().to_string(), format!("{}", rec.cigar()), rec.cigar().len().to_string())
} else {
("NA".to_string(), "NA".to_string(), "NA".to_string(), "NA".to_string())
};
println!("{:?},{:?},{:?},{},{},{},{}", std::str::from_utf8(&read).unwrap(), new_now.duration_since(now), record.len(), chr, pos, cigar, cigar_ops);
if record.len() > 0 {
let rec = &record[0];
println!("{:?},{:?},{:?},{},{},{},{}", std::str::from_utf8(&read).unwrap(), new_now.duration_since(now), record.len(), rec.tid(), rec.pos(),rec.cigar(), rec.cigar().len())
} else {
println!("{:?},{:?},{:?},NA,NA,NA,NA", std::str::from_utf8(&read).unwrap(), new_now.duration_since(now), record.len())
};

Though I guess it doesn't really matter if this is just temporary benchmarking code.

But, maybe this should be an actual benchmark?

record

}

/// Aligns a given read and return the resulting SAM string
Expand Down