Add CLI progress bars and throughput metrics to partitioning
Add `indicatif` v0.17 to `obikmer` and `obikpartitionner` to instrument CLI workflows with real-time progress tracking. The changes integrate progress spinners and bars into the batch processing and parallel kmer counting loops, displaying processed base pairs, throughput rates, and elapsed time. Updates occur every 0.1s to enhance observability without modifying core partitioning logic.
This commit is contained in:
Eric Coissac
Generated
+56
@@ -489,6 +489,19 @@ dependencies = [
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"impl-tools 0.11.4",
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]
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[[package]]
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name = "console"
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version = "0.15.11"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "054ccb5b10f9f2cbf51eb355ca1d05c2d279ce1804688d0db74b4733a5aeafd8"
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dependencies = [
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"encode_unicode",
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"libc",
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"once_cell",
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"unicode-width",
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"windows-sys 0.59.0",
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]
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[[package]]
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name = "core-foundation-sys"
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version = "0.8.7"
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@@ -747,6 +760,12 @@ version = "1.15.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "48c757948c5ede0e46177b7add2e67155f70e33c07fea8284df6576da70b3719"
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[[package]]
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name = "encode_unicode"
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version = "1.0.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "34aa73646ffb006b8f5147f3dc182bd4bcb190227ce861fc4a4844bf8e3cb2c0"
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[[package]]
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name = "enum-as-inner"
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version = "0.6.1"
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@@ -1216,6 +1235,19 @@ dependencies = [
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"hashbrown 0.17.0",
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]
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[[package]]
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name = "indicatif"
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version = "0.17.11"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "183b3088984b400f4cfac3620d5e076c84da5364016b4f49473de574b2586235"
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dependencies = [
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"console",
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"number_prefix",
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"portable-atomic",
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"unicode-width",
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"web-time",
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]
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[[package]]
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name = "infer"
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version = "0.19.0"
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@@ -1689,6 +1721,12 @@ dependencies = [
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"autocfg",
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]
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[[package]]
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name = "number_prefix"
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version = "0.4.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
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[[package]]
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name = "obicompactvec"
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version = "0.1.0"
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@@ -1723,6 +1761,7 @@ name = "obikmer"
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version = "0.1.0"
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dependencies = [
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"clap",
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"indicatif",
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"memmap2",
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"niffler 3.0.0",
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"obidebruinj",
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@@ -1748,6 +1787,7 @@ version = "0.1.0"
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dependencies = [
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"cacheline-ef",
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"epserde 0.8.0",
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"indicatif",
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"memmap2",
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"niffler 3.0.0",
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"obicompactvec",
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@@ -2934,6 +2974,12 @@ version = "1.0.24"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "e6e4313cd5fcd3dad5cafa179702e2b244f760991f45397d14d4ebf38247da75"
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[[package]]
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name = "unicode-width"
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version = "0.2.2"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "b4ac048d71ede7ee76d585517add45da530660ef4390e49b098733c6e897f254"
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[[package]]
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name = "untrusted"
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version = "0.9.0"
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@@ -3111,6 +3157,16 @@ dependencies = [
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"wasm-bindgen",
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]
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[[package]]
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name = "web-time"
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version = "1.1.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "5a6580f308b1fad9207618087a65c04e7a10bc77e02c8e84e9b00dd4b12fa0bb"
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dependencies = [
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"js-sys",
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"wasm-bindgen",
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]
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[[package]]
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name = "webpki-roots"
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version = "0.26.11"
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@@ -23,6 +23,7 @@ niffler = "3"
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rayon = "1"
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ph = "0.11"
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memmap2 = "0.9"
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indicatif = "0.17"
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tracing = "0.1.44"
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tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }
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pprof = { version = "0.13", features = ["prost-codec"], optional = true }
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@@ -1,6 +1,8 @@
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use std::path::PathBuf;
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use std::time::{Duration, Instant};
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use clap::Args;
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use indicatif::{ProgressBar, ProgressStyle};
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use obikpartitionner::KmerPartition;
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use obisys::{Reporter, Stage};
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use obikseq::{RoutableSuperKmer, set_k, set_m};
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@@ -49,12 +51,45 @@ pub fn run(args: PartitionArgs) {
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|? { move |rope| obiread::normalize_sequence_chunk(rope, k) } : RawChunk => NormChunk,
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| { move |rope| obiskbuilder::build_superkmers(rope, k, level_max, theta) }: NormChunk => Batch,
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};
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let pb = ProgressBar::new_spinner();
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pb.set_style(
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ProgressStyle::with_template("{spinner} scatter — {msg} {elapsed}")
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.unwrap()
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.tick_strings(&["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"]),
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);
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pb.enable_steady_tick(Duration::from_millis(100));
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let mut total_bases: u64 = 0;
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let mut ema_rate: f64 = 0.0;
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let mut last_t = Instant::now();
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let mut last_bases: u64 = 0;
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const ALPHA: f64 = 0.15;
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for batch in pipe.apply(path_source, n_workers, 1) {
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total_bases += batch.iter().map(|sk| sk.seql() as u64).sum::<u64>();
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let now = Instant::now();
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let dt = now.duration_since(last_t).as_secs_f64();
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if dt > 0.1 {
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let instant = (total_bases - last_bases) as f64 / dt;
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ema_rate = ALPHA * instant + (1.0 - ALPHA) * ema_rate;
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last_t = now;
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last_bases = total_bases;
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let bp = total_bases as f64;
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let (count_str, rate_str) = if bp >= 1e9 {
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(format!("{:.2} Gbp", bp / 1e9), format!("{:.0} Mbp/s", ema_rate / 1e6))
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} else {
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(format!("{:.0} Mbp", bp / 1e6), format!("{:.0} Mbp/s", ema_rate / 1e6))
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};
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pb.set_message(format!("{count_str} {rate_str}"));
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}
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kp.write_batch(batch).unwrap_or_else(|e| {
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eprintln!("error: {e}");
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std::process::exit(1)
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});
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}
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pb.finish_and_clear();
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kp.close().expect("close error");
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rep.push(t.stop());
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@@ -25,3 +25,4 @@ epserde = "0.8"
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memmap2 = "0.9.10"
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obicompactvec = { path = "../obicompactvec" }
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ptr_hash = "1.1"
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indicatif = "0.17"
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@@ -2,7 +2,10 @@ use std::collections::{BTreeMap, HashMap};
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use std::fs;
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use std::io;
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use std::path::{Path, PathBuf};
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use tracing::{debug, info};
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use std::time::Instant;
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use tracing::debug;
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use indicatif::{ProgressBar, ProgressStyle};
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use cacheline_ef::{CachelineEf, CachelineEfVec};
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use epserde::ser::Serialize as EpSerialize;
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@@ -55,7 +58,7 @@ impl KmerPartition {
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minimizer_size: usize,
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force: bool,
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) -> SKResult<Self> {
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Self::create_with(path, n_bits, kmer_size, minimizer_size, Level::Three, force)
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Self::create_with(path, n_bits, kmer_size, minimizer_size, Level::One, force)
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}
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pub fn create_with<P: AsRef<Path>>(
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@@ -256,18 +259,33 @@ impl KmerPartition {
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let n_threads = rayon::current_num_threads().max(1) as u64;
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let chunk_kmers = chunk_size_from_ram(available / n_threads);
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let pb = ProgressBar::new(self.n_partitions as u64);
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pb.set_style(
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ProgressStyle::with_template(
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"counting [{bar:40}] {pos}/{len} ({percent}%) {per_sec} eta {eta} {msg}",
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)
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.unwrap()
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.progress_chars("█▌░"),
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);
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let results: Vec<SKResult<()>> = (0..self.n_partitions)
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.into_par_iter()
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.map(|i| {
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let dir = root.join(format!("part_{:05}", i));
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let dedup_path = dir.join(format!("dereplicated.{SK_EXT}"));
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if !dedup_path.exists() {
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pb.inc(1);
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return Ok(());
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}
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info!("counting kmers in partition {}/{}", i, self.n_partitions);
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count_partition(&dir, &dedup_path, chunk_kmers)
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let t = Instant::now();
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let result = count_partition(&dir, &dedup_path, chunk_kmers);
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pb.set_message(format!("last {:.0}ms", t.elapsed().as_millis()));
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pb.inc(1);
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result
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})
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.collect();
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pb.finish_and_clear();
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for r in results {
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r?;
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}
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