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feat(progress-logger): added a progress logger #10

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merged 1 commit into from
Aug 6, 2022
Merged

feat(progress-logger): added a progress logger #10

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14 changes: 12 additions & 2 deletions Cargo.lock
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1 change: 1 addition & 0 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ log = "0.4.14"
mimalloc = {version = "0.1.26", default-features = false}
num_cpus = "1.13.0"
parking_lot = "0.11.2"
proglog = "0.2.0"
rayon = "1.5.1"
regex = "1.5.4"
seq_io = "0.3.1"
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13 changes: 11 additions & 2 deletions src/main.rs
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Expand Up @@ -19,6 +19,7 @@ use itertools::{self, izip, Itertools};
use lazy_static::lazy_static;
use log::info;
use parking_lot::Mutex;
use proglog::ProgLogBuilder;
use rayon::prelude::*;
use regex::{Regex, RegexBuilder};
use seq_io::fastq::{self, OwnedRecord};
Expand Down Expand Up @@ -333,6 +334,13 @@ struct Barcode<'a>(&'a [u8], &'a [u8]);
#[allow(clippy::too_many_lines)]
fn main() -> Result<()> {
let opts = setup();
let progress_logger = ProgLogBuilder::new()
.name("fqgrep-progress")
.noun("reads")
.verb("Searched")
.unit(50_000_000)
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Shall we separate with comma's (there's a crate for that)?

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Sure! I'll put it behind a feature flag I think to keep proglog low dependency by default, but agree tidier numbers would be nice.

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I am not going to hold this PR up, thank-you @sstadick !

.build();

let ref_sample = Sample::from_r1_path(&opts.r1_fastq, REF_PREFIX)?;
let alt_sample = Sample::from_r1_path(&opts.r1_fastq, ALT_PREFIX)?;
let both_sample = Sample::from_r1_path(&opts.r1_fastq, BOTH_PREFIX)?;
Expand Down Expand Up @@ -379,6 +387,7 @@ fn main() -> Result<()> {
(false, true) => Matches::Alt,
(false, false) => Matches::None,
};
progress_logger.record();
(m, (r1, r2))
})
.filter(|(m, _)| *m != Matches::None)
Expand Down Expand Up @@ -406,7 +415,7 @@ fn main() -> Result<()> {
)
.for_each(
|(ref_reads, alt_reads, both_reads): MatchedReads| {
// Aquire lock to ensure R1 and R2 are enqueued at the same time
// Acquire lock to ensure R1 and R2 are enqueued at the same time
{
let _lock = ref_writer.lock.lock();
ref_writer.r1.tx.as_ref().unwrap().send(ref_reads.0).expect("Failed to send R1s");
Expand Down Expand Up @@ -475,7 +484,7 @@ fn main() -> Result<()> {
.handle
.join()
.expect("Error joining r2 handle");

drop(progress_logger);
info!(
"{} reads matched input ref sequence",
ref_r1_stats.reads_written
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