sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a9489632aa0750e457baa9c3e5eff5bdaa254c7a4ad4343e224f3180db7f0204 | Rust | 751 | 38 | #[cfg(target_os = "android")]
pub mod android;
use anyhow::Result;
#[derive(Clone, Debug)]
pub struct PickedFile {
pub data: Vec<u8>,
pub file_name: String,
}
#[cfg(not(target_os = "android"))]
pub async fn pick_file_rfd() -> Result<PickedFile> {
use anyhow::Context;
let file = rfd::AsyncFileDialog::... |
56830e90b188e89cb76564ae8d833e8b7cb4778527b610062d5421404f0b1cb5 | Rust | 785 | 28 | //! Minimal STDERR logger. Diagnostics are never part of the byte-identity gate;
//! `--verbose` gates the extra detail. Mirrors `bismark-genome-preparation`.
/// Tiny logger: `note` always prints (Perl `warn`-level); `info` only with
/// `--verbose` (Perl `$verbose and print`).
#[derive(Debug, Clone, Copy)]
pub struc... |
e65a00c587423b4a2b1ce38c75d666b556d733eafc0c010f59bef04e9c11d067 | Rust | 800 | 33 | pub(crate) struct CodeWriter {
state: String,
indent: usize,
}
impl CodeWriter {
pub(crate) fn new() -> Self {
Self {
state: String::new(),
indent: 0,
}
}
pub(crate) fn add_line<T: AsRef<str>>(&mut self, line: T) {
self.indent -= line.as_ref().chars(... |
d40fc530f3ccaf03bdd5f8dfd01e982661c4aef239de3ab6551746f4a4961f1e | Rust | 868 | 19 | //! Permit pool for concurrent slot management.
//!
//! The permit system uses typestate to enforce valid state transitions at compile time:
//! - `PermitInUse` → `PermitIdle` via `into_idle()` (returns to pool on drop)
//! - `PermitInUse` → `PermitPoisoned` via `into_poisoned()` (orphaned on drop)
//! - `PermitPoisone... |
e67f59b633defbbd56efc11439733cd0e20cd312fb02e411cf09d17eac9b44eb | Rust | 1,034 | 36 | #![cfg(target_os = "android")]
use jni::sys::{jint, JNI_VERSION_1_6};
use std::os::raw::c_void;
use std::sync::Arc;
#[allow(non_snake_case)]
#[no_mangle]
pub extern "system" fn JNI_OnLoad(vm: jni::JavaVM, _: *mut c_void) -> jint {
let vm_ref = Arc::new(vm);
rrfd::android::jni_initialize(vm_ref);
JNI_VERSIO... |
55aa8a77030862b7e9ca662e9d3e88a44fb0602850f85e9cd82552090f937d12 | Rust | 1,048 | 24 | //! Typed errors for `bismark-report`.
//!
//! `main` maps any of these to exit code `1`; clap parse errors map to `2`
//! (clap convention). None of the error *text* is part of the byte-identity
//! gate — diagnostics go to STDERR only.
#[derive(Debug, thiserror::Error)]
pub enum ReportError {
/// Direct `std::io... |
640eb67cd13aeb06cdd7160d49e8e51c00d7628cb9ab87d3352d84aa782b6946 | Rust | 1,091 | 28 | //! # Bismark — the whole bisulfite-sequencing suite (Rust): one crate, one binary.
//!
//! Every tool is a module here (`bismark::bam2nuc`, `bismark::dedup`, …), folded
//! from the former 14 crates (epic `plans/07062026_single-binary-suite/`). The
//! multicall CLI + classic-name aliases are wired in Phase 3; during ... |
2e8c8ba8b1938a0e515ee27a20aa0d64fbc3a293057621eaab1d3c872c2d4ac7 | Rust | 1,157 | 30 | //! methylseq CLI-surface conformance — `BISMARK_REPORT` (nf-core/methylseq **4.2.0**).
//!
//! Asserts the Rust `bismark2report` CLI accepts the command methylseq's report
//! module emits. See `plans/06122026_methylseq-cli-conformance/`.
//!
//! **Command template** (`modules/nf-core/bismark/report/main.nf`;
//! `con... |
24cd4250e48bcea551c3dd521c8ce8fe3d3d3d5279419b3c35979bdfd310e2fa | Rust | 1,209 | 31 | // Autogenerated by brush-wgsl from source wgsl files. Do not edit.
#![allow(dead_code, unused_mut, clippy::all)]
fn create_composer() -> naga_oil::compose::Composer {
let mut composer = naga_oil::compose::Composer::default().with_capabilities(
naga::valid::Capabilities::SUBGROUP |
naga::val... |
c6fd01b3b0268fda85cf823874e105f9d5248b287adffd08838ab7765dbf8a59 | Rust | 1,266 | 28 | //! Tripwire: the checked-in `docs/images/bismark_summary_report.html` is the
//! STALE v0.15.2 Highcharts-era report (zero `Plotly` tokens). The acceptance
//! oracle must be a fresh run of the current Perl `bismark2summary` — never
//! this file. This test fails loudly if that committed HTML ever gains a
//! `Plotly`... |
b1e4891eeb5fbbe35f85a46a29280a8b22c9040add1598120a706d6e69fb3c22 | Rust | 1,308 | 50 | use std::sync::atomic::{AtomicBool, Ordering};
use tracing::{info_span, Subscriber};
use tracing_subscriber::layer::{Context, Layer};
use tracing_subscriber::registry::LookupSpan;
use burn_wgpu::{Wgpu, WgpuDevice};
// Global flag to enable/disable sync
static SYNC_ENABLED: AtomicBool = AtomicBool::new(false);
// Tr... |
bb2780990cc4e88f73e7fe63c535cada44259b6ce332f3d0a1af30b900ad20dd | Rust | 1,347 | 40 | //! THROWAWAY SPIKE (filter_non_conversion port) — NOT shipped code.
//!
//! Question: does a pure noodles `RecordBuf` -> BAM round-trip preserve the
//! alignment-record body byte-identically vs samtools' own reference, so a
//! verbatim-passthrough filter can rely on it for byte-identity?
//!
//! Run: cargo run -p bi... |
9a99ec14dd6b318a0a29908bde43549ba42066e810a8ac3478a28437abc16fa3 | Rust | 1,349 | 39 | //! Step IV (opt, `--combined_genome`): the Bismark-Rust combined-reference
//! extension. Additive — runs after the standard CT/GA outputs + indices.
//!
//! Writes `Bisulfite_Genome/Combined/genome_mfa.combined.fa` (all CT-converted
//! records, then all GA-converted records — built directly from the converted
//! st... |
0a7bc4f212a046d408963cb5c4522be5beb2269ad5f1c672685242b9015f5488 | Rust | 1,378 | 54 | use brush_render::{camera::Camera, Backend};
use burn::tensor::Tensor;
#[derive(Debug, Default, Clone)]
pub struct SceneView {
pub camera: Camera,
pub image: image::DynamicImage,
}
// Encapsulates a multi-view scene including cameras and the splats.
// Also provides methods for checkpointing the training proc... |
9ba1bc70fd190a3dd6c7850a9d51a465b49de12bc58793567744a0acc8ae62bc | Rust | 1,384 | 55 | #[derive(Debug, Default, Clone)]
pub struct Camera {
pub fov: glam::Vec2,
pub center_uv: glam::Vec2,
pub position: glam::Vec3,
pub rotation: glam::Quat,
}
impl Camera {
pub fn new(
position: glam::Vec3,
rotation: glam::Quat,
fov: glam::Vec2,
center_uv: glam::Vec2,
... |
85f236ea8465b3ddfb3ce5347b928d5f1848333b50bbafe1f80608f3a8ff0ad1 | Rust | 1,459 | 42 | //! methylseq CLI-surface conformance — `BISMARK_SUMMARY` (nf-core/methylseq **4.2.0**).
//!
//! Asserts the Rust `bismark2summary` CLI accepts the command methylseq's summary
//! module emits. See `plans/06122026_methylseq-cli-conformance/`.
//!
//! **Command template** (`modules/nf-core/bismark/summary/main.nf`;
//! ... |
4763552c6a8b02fdcd48e93aeab0bace99b9f9419c6d5e7a135562477cd5d257 | Rust | 1,466 | 41 | //! `bismark-io` — Bismark-aware BAM/SAM/CRAM I/O on top of [`noodles`].
//!
//! This crate is the shared library for Bismark's Rust rewrite, exposing
//! Bismark-flavoured wrappers around [`noodles`] record types — strand-
//! classified, tag-decoded, CIGAR-aware.
//!
//! See `DESIGN.md` (in the crate root) for the de... |
e09cc30567a6bf0714b68eee839741fe6d5052adfeca0d85190167e65d0b3bd4 | Rust | 1,588 | 43 | //! Drift guard: the committed `summary_template.html` MUST equal the inline
//! single-quoted heredoc in the Perl `bismark2summary` source. If the Perl
//! template is ever edited, this fails loudly so the embedded copy is
//! refreshed. Auto-skips when the Perl source is unavailable.
use std::path::Path;
const TEMP... |
611f5d5138c1287e5398d3fbe2d6f4980af5fef58f37fde97251c538aeeac8ca | Rust | 1,612 | 53 |
fn main() -> anyhow::Result<()> {
let wgpu_options = brush_viewer::wgpu_config::get_config();
#[cfg(not(target_arch = "wasm32"))]
{
// Build app display.
let native_options = eframe::NativeOptions {
viewport: egui::ViewportBuilder::default()
.with_inner_size(egu... |
805194c24f19a030aa82882e0450f73a0bb2f460560407949db26e2a99a013c0 | Rust | 1,687 | 40 | //! SAM header → ASCII chromosome-name lookup table.
//!
//! Built once per input file at `extract_se` entry. Mirrors `bismark-dedup`'s
//! refid-table pattern (`pipeline.rs:64-82`) but returns chr **names** rather
//! than interned u32 ids — the extractor's output lines embed the literal
//! chr string.
//!
//! Per Re... |
360ef79702d5df81233050be86c3cd3df0ef4f3d5824013ca145830968ef2651 | Rust | 1,782 | 76 | use burn_jit::{JitElement, JitRuntime};
use burn_wgpu::JitTensor;
use std::collections::HashMap;
#[derive(Clone, Copy)]
pub(crate) enum DimBound {
Exact(usize),
Any,
Matching(&'static str),
}
pub(crate) struct DimCheck<'a, R: JitRuntime> {
bound: HashMap<&'a str, usize>,
device: Option<R::Device>,... |
cf42cf94ca9b395acf592ef4b83cb6efff5cbaeaceaf3dce969f223aad397953 | Rust | 1,910 | 63 | pub mod colmap;
pub mod colmap_read_model;
pub mod nerf_synthetic;
pub mod scene_batch;
use std::path::{Path, PathBuf};
use anyhow::Result;
use brush_train::scene::SceneView;
use burn::{
prelude::Backend,
tensor::{Tensor, TensorData},
};
use image::{DynamicImage, GenericImageView};
pub(crate) fn normalized_p... |
c0dcd618c15352923ddd2249032d8e3ed7d06fce865a06c7726c722f112df138 | Rust | 1,965 | 45 | //! Deterministic `.txt` golden test — runs the built binary end-to-end and
//! asserts the byte-exact table. Needs **no** Perl (the `.txt` is pure
//! pass-through), so it gates the table on every CI runner.
mod common;
use std::process::Command;
#[test]
fn wgbs_two_sample_txt_is_byte_exact() {
let dir = tempfi... |
722f658313b6855e74a8cecdbd11c2058583c2571cfa4b149a31f45e91992cdf | Rust | 2,029 | 47 | //! Typed errors for `bismark-nome-filtering`.
//!
//! Produced at the CLI / orchestration boundary. Genome-load failures
//! propagate from the promoted [`crate::io::genome`] reader via the
//! [`BismarkNomeError::Genome`] `#[from]` variant — note these come from the
//! module-local `GenomeError`, NOT from `crate::io... |
d59849a6672c9ab441f0647499a7f3bc91ae0594cd860cf78798dd9ae00f5cfc | Rust | 2,032 | 67 | //! Phase A integration sanity tests for `coverage2cytosine_rs`.
//!
//! Spawns the built binary and asserts the minimum Phase-A bar: it builds,
//! prints a recognisable `--version` provenance string, lists the v1.0 flags
//! in `--help`, and fails clearly on bad invocations.
use assert_cmd::Command;
use predicates::... |
b605038f65c49a8e1ce38ef1f2a133f15c801ee9f759f552d7a9eaba35e4b198 | Rust | 2,039 | 53 | //! methylseq CLI-surface conformance — `BISMARK_GENOMEPREPARATION`
//! (nf-core/methylseq **4.2.0**).
//!
//! Asserts the Rust `bismark_genome_preparation` CLI accepts every command
//! methylseq's genome-prep module emits. See `plans/06122026_methylseq-cli-conformance/`.
//!
//! **Command template** (`modules/nf-core... |
f98d59827003c811a7db11794730d96fa3190f0bc073757e359363eb325aadbe | Rust | 2,082 | 55 | //! Argument-struct types for the extraction kernel.
//!
//! Per SPEC §6.3 + §7.7: typed parameter structs replace the 14-arg
//! `extract_calls` signature seen in the prior-art Rust port. Adding a
//! new flag = adding a typed field, not appending to a positional list.
//!
//! Phase A: defines the struct shape. Field-... |
581a889bd4e4bf35d43c65cc10d3fdb918288a6b76bceb3949da6ee2fba438cd | Rust | 2,128 | 59 | //! Real-data smoke (`#[ignore]`) for the oxy byte-identity gate.
//!
//! The AUTHORITATIVE real-data gate is `scripts/bam2nuc_byte_identity.sh`, which
//! runs BOTH the Rust `bam2nuc_rs` and the Perl `bam2nuc` v0.25.1 over a real
//! genome + BAMs and diffs the outputs byte-for-byte (see that script's header
//! for t... |
c0c9bb553479015ca42a2932d1785d76c6b18958bb5fb0dd269a4e9b1257a474 | Rust | 2,204 | 63 | //! Step I output tree: `<genome>/Bisulfite_Genome/{CT,GA}_conversion/`.
use std::path::{Path, PathBuf};
use crate::genome_prep::error::GenomePrepError;
use crate::genome_prep::logging::Logger;
/// Create the `Bisulfite_Genome/{CT,GA}_conversion/` tree under `genome_folder`.
/// If `Bisulfite_Genome/` already exists... |
5be327010145b9731250b50ca62006c00a1301ce744e1833ff599922d476da29 | Rust | 2,222 | 70 | use burn::tensor::{backend::Backend, module::conv2d, ops::ConvOptions, Tensor};
fn gaussian<B: Backend>(window_size: usize, sigma: f32, device: &B::Device) -> Tensor<B, 1> {
let sigma2 = 2.0 * sigma.powf(2.0);
let window_extent = (window_size / 2) as f32;
let gauss_floats: Vec<_> = (0..window_size)
... |
845ae89b40be571c27c69e91507e7e92725a6e7426a07ee4f504342cae30a0de | Rust | 2,225 | 78 | //! coglet: Rust execution engine for cog models.
mod health;
pub mod input_validation;
mod prediction;
mod predictor;
mod version;
pub mod bridge;
mod fd_redirect;
pub mod orchestrator;
pub mod permit;
pub mod service;
mod setup_log_accumulator;
#[cfg(feature = "tracing")]
pub mod trace;
pub mod transport;
pub mod w... |
e8bc794fbb16776704086f5b91a1fdbd88cda3ac4edce2760223cc6115e4bce6 | Rust | 2,264 | 81 | //! Tracing layer that accumulates all logs from coglet server during setup.
//!
//! Captures every tracing event from the moment the server starts until setup completes.
//! This includes:
//! - Initial server startup logs ("coglet <version>")
//! - Orchestrator logs ("Spawning worker subprocess")
//! - Re-emitted wor... |
bd58a28ad853d29183782f47a6cd121b35e91360e63f9155ae5aea61c309895b | Rust | 2,336 | 76 | use brush_render::camera::Camera;
use glam::{Mat3, Quat, Vec2, Vec3};
pub struct OrbitControls {
pub focus: Vec3,
pub radius: f32,
pan_momentum: Vec2,
rotate_momentum: Vec2,
}
impl OrbitControls {
pub fn new(radius: f32) -> Self {
Self {
focus: Vec3::ZERO,
radius,
... |
888a258bcf7bc535c0fa8b57fdb1f54e7cebaf23c80ce952194f24389f51b196 | Rust | 2,462 | 57 | //! #1025 Phase 1 — real-data regression guard for the uBAM transcoder.
//!
//! Uses genuine **Trim Galore 2.2.0 `--output-format ubam`** output (subsampled to 200
//! single-end reads / 200 collated paired-end pairs from the 10K `test_files/` BAMs) and
//! asserts the in-process transcode (`ubam::transcode_ubam_to_fas... |
f72f12ba7ce0c6e6b2591e9a2a28265db7e9b150096eac6e863c3dd34a91f4e9 | Rust | 2,484 | 68 | //! Command-line surface (clap derive).
//!
//! Flag spellings match the Perl `bismark2report` exactly (underscores
//! preserved: `--alignment_report`, `--dedup_report`, `--splitting_report`,
//! `--mbias_report`, `--nucleotide_report`). `--version`/`--man` are handled
//! manually (clap's auto-version is disabled) so... |
790aa44e8f0be1600974505ac6e85090bb5a5593a747e4edd9ea04b036369cda | Rust | 2,514 | 61 | // Autogenerated by brush-wgsl from source wgsl files. Do not edit.
#![allow(dead_code, unused_mut, clippy::all)]
fn create_composer() -> naga_oil::compose::Composer {
let mut composer = naga_oil::compose::Composer::default().with_capabilities(
naga::valid::Capabilities::SUBGROUP |
naga::val... |
a52241b7aff1a8b4f3a28f04fc24cc265d26ab02bf4efdb42693e7424bda06f2 | Rust | 2,516 | 78 | //! Faithful reproduction of Perl's `substr(EXPR, OFFSET, LEN)` rvalue
//! semantics (SPEC §9).
//!
//! The sole caller passing a possibly-negative offset is the reverse-read
//! genome-window extraction in Phase B (`substr(chr, last_end-3, …)` for a
//! reverse read whose rightmost coordinate is at chromosome position... |
d9c4244f272287e87d8d2430b43fb3e26801b93e3ccd6696c248afece57f38f1 | Rust | 2,533 | 67 | //! Function-level micro-benchmark for `SamRecord::parse` (06222026 perf epic).
//!
//! The parse byte-split's win is real but below the end-to-end noise floor
//! (the aligner is ~90% bowtie2-bound under `-p`; GATE_00). This bench isolates
//! it: it compares the current byte-scan field split against the pre-epic
//! ... |
1b542e373cccacd5a912ac899cd5be810ca79edd5b205ee91663afdb0a2f13f8 | Rust | 2,632 | 65 | //! Typed errors for `bismark-genome-preparation`.
//!
//! The binary's `main` maps any of these to exit code `1`; clap parse errors
//! map to `2` (clap convention). None of the error *text* is part of the
//! byte-identity gate (diagnostics are STDERR).
use std::path::PathBuf;
/// All errors raised by the genome-pr... |
01ee3f4fbc00c848ff9620b8a4b088757d608ef679980d5c220219641975029d | Rust | 2,637 | 90 | //! Phase A integration tests for the `NOMe_filtering_rs` binary.
//!
//! Covers the boot surface: `--version`, the `--merge_CpGs`+`--CX` die, the
//! mandatory-genome die, and a valid invocation that loads a tiny synthetic
//! genome and exits 0. Per-read processing + output is Phase B (not tested here
//! — Phase A's... |
b88981ed37d9a8b1d438525f703b6b0247dc87523716c9b7b98b36d1698cf264 | Rust | 2,803 | 92 | //! Output-filename derivation matching Perl `NOMe_filtering` (`:464-468` plus
//! the force-`.gz` at `:74-76`).
//!
//! The Perl chain is:
//! ```text
//! $out = $infile;
//! $out =~ s/\.gz$//; # strip ONE trailing .gz
//! $out =~ s/\.txt$//; # strip ONE trailing .txt
//! $out =~ s/$/.manOwar.txt/; #... |
e6bebcb46039b5e4bebd3c0985dd9c2bc74f56ed70a7b2b65eb7d0e1dd706cae | Rust | 2,835 | 83 | //! Methylation-call validation, mirroring Perl `validate_methylation_call`
//! (`bismark2bedGraph:558-588`).
//!
//! The branch (CpG vs non-CpG) is chosen by the call letter: Perl tests
//! `$meth_state2 =~ /^z/i` (`:564`), so a call starting with `z`/`Z` takes
//! the CpG branch. Comparisons are **full-field string e... |
97c9bb08f0939c2dc479c93bacfdf16bc0741d3f626858da1d6afd6e91d4ca8e | Rust | 2,849 | 94 | //! Optional `--ucsc` post-pass (Perl `bismark2bedGraph:514-552`).
//!
//! Re-reads the just-written bedGraph and emits a UCSC-compatible variant
//! (`{out}_UCSC.bedGraph.gz`): the header line is copied verbatim; for each
//! data line the chromosome name is transformed — `MT` → `chrM`, and any
//! name not already st... |
f913540eb65435e52f8847844f9108f8278b6221b12aa94238f840fb0ac9e42f | Rust | 2,896 | 86 | use brush_render::camera::{self, Camera};
use brush_train::scene::SceneView;
use std::io::{Cursor, Read};
use crate::colmap_read_model;
#[allow(unused_variables)]
pub fn read_dataset(
zip_data: &[u8],
max_frames: Option<usize>,
max_resolution: Option<u32>,
) -> anyhow::Result<Vec<SceneView>> {
let mut... |
4f5271b5944988c918bfb2536e4cc732f42ecb827855131e765d206bd7dbd5f1 | Rust | 2,976 | 70 | //! Typed errors for `bismark-methylation-consistency`.
//!
//! Produced at the CLI-validation and pipeline-orchestration boundaries.
//! Library errors from [`bismark_io`] propagate via the
//! [`MethConsError::Io`] variant. `main` maps any of these to exit code 1;
//! clap parse errors exit 2 (clap convention). None ... |
f50f026b60cff6ddd044ea3755f652ccf55aec31c3b02e0e0ee9354c6ac301bd | Rust | 3,006 | 78 | //! `bismark-methylation-consistency` — Rust port of Bismark Perl's
//! `methylation_consistency` script.
//!
//! Splits a Bismark alignment BAM into three BAMs by the **read-level**
//! consistency of its CpG (or, with `--chh`, CHH) methylation calls —
//! consistently methylated (`>= upper_threshold`), consistently u... |
a96328175dd5fd83d8337681fb54a94390fbe99dad7cf6db3e1604d6f71bd0f5 | Rust | 3,029 | 98 | //! The tab-delimited `bismark_summary_report.txt` table.
//!
//! Perl `bismark2summary:228-246` (header), `:387-404` (rows), `:478-481`
//! (write). One row per sample in discovery/argv order, 15 tab-separated
//! columns, header + each row `\n`-terminated. Values are the **raw**
//! captured strings (empty = not foun... |
9f33e397add6251e6e7cddcf422ca84b2bfe26911ff7504f8bd04fbf52ce268d | Rust | 3,037 | 94 | //! Output-filename derivation, faithful to Perl `bam2nuc` `:147-152`.
//!
//! ```text
//! $outfile = basename($infile); # s/.*\///
//! die unless $outfile =~ s/(bam|cram)$/nucleotide_stats.txt/;
//! ```
//!
//! Two quirks replicated exactly:
//! - **No dot anchor:** the regex strips a trailing `bam`/`c... |
97e05a2a9e85178878e20abba073900bab85e6d3b3fd19a77350120b89590295 | Rust | 3,082 | 102 | //! Phase A sanity tests.
//!
//! Spawns the `bismark_methylation_extractor` binary with basic flags
//! and asserts the binary boots correctly + `--help` lists all 35 flags
//! + `--version` matches the provenance regex.
use assert_cmd::Command;
use predicates::str::is_match;
#[test]
fn version_output_matches_proven... |
0e8c6571d9d0c3bf57408c206e8dac739a4c296f95c5bc998b6e1e47c777f385 | Rust | 3,089 | 92 | //! STDERR diagnostics — a logger gated by `--quiet`.
//!
//! All diagnostic output goes to STDERR, matching Perl `methylation_consistency`'s
//! `warn` model (stdout stays clean; only `--version` writes to stdout, in
//! `main.rs`). These messages are NOT part of the byte-identity gate (SPEC §7)
//! — they mirror Perl... |
7bc2eea8ba67adc58089d5482c858de13bd1bc1d71e0073ae7eaf6278c1c26ad | Rust | 3,100 | 76 | //! Typed errors for `bismark-aligner` (Phase 1: CLI / discovery / aligner
//! detection).
//!
//! `main` maps any of these to exit code `1`; clap parse errors map to `2`
//! (clap convention). None of the error *text* is part of the byte-identity
//! gate (diagnostics go to STDERR), but messages mirror Perl `die`s whe... |
5fa8504c269df0e3aa20a0a373ff46f4f3fe1241e5365d93c5350a60b34e3f8f | Rust | 3,133 | 96 | //! Output-filename derivation matching Perl `filter_non_conversion`
//! (`process_file`, lines 85–98).
//!
//! The Perl chain for each output is:
//! ```text
//! my $outfile = $infile; # the CLI arg verbatim — NO directory strip
//! $outfile =~ s/\.bam$//; # strip a single trailing ".bam" (dot-anchored)
/... |
05b70fa8abc934ce2230cfbe8fcb71a7deebffea600076f181ed0a5e592992e6 | Rust | 3,140 | 91 | use brush_render::camera::Camera;
use brush_render::Backend;
use burn::tensor::Tensor;
use brush_train::scene::Scene;
use brush_train::scene::SceneBatch;
use crate::image_to_tensor;
pub struct SceneLoader<B: Backend> {
images: Vec<Tensor<B, 3>>,
cameras: Vec<Camera>,
index: usize,
batch_size: usize,
... |
85ea58cebb21bfd5124710370bf871a7c6c72db9eade1efe620701aee5c9f85e | Rust | 3,215 | 85 | //! Generate Python stub files for coglet.
//!
//! Run with: cargo run --bin stub_gen
//!
//! Custom generate logic: pyo3-stub-gen places classes from the native
//! `coglet._impl` module into the `coglet` parent package stub. We redirect
//! that output to `coglet/_impl.pyi` so native module types are preserved in
//... |
39e3653e915e38220ce86eb95dfb73bb25113d5e9409d3d14cb46d9fb2625666 | Rust | 3,229 | 93 | #![allow(clippy::too_many_arguments)]
#![allow(clippy::single_range_in_vec_init)]
use brush_kernel::bitcast_tensor;
use burn::backend::Autodiff;
use burn::tensor::{ElementConversion, Int, Tensor};
use burn_jit::JitBackend;
use burn_wgpu::{JitTensor, WgpuRuntime};
use camera::Camera;
mod dim_check;
mod kernels;
mod saf... |
385e3661d5cb94d204d6ac651b6c5f8b297d36191b00242da807f5005395df13 | Rust | 3,304 | 84 | use super::PickedFile;
use anyhow::Result;
use async_channel::Sender;
use jni::objects::{GlobalRef, JByteArray, JClass, JStaticMethodID, JString};
use jni::signature::Primitive;
use jni::JNIEnv;
use lazy_static::lazy_static;
use std::sync::Arc;
use std::sync::RwLock;
lazy_static! {
static ref VM: RwLock<Option<Arc... |
3ec94b691d8710a6673eb6a09d78797fa37dfac8a2a9279adcb3023a67251890 | Rust | 3,366 | 97 | //! `{{date}}` / `{{time}}` generation — the report's only non-determinism.
//!
//! Two paths (PLAN A6, zero new dependency trees):
//! * **deterministic** (`--__test_timestamp <epoch>`): format the epoch in
//! **UTC** with pure-std integer civil-time math → byte-stable golden HTML.
//! * **default** (`None`): local... |
dafd19ab8685e6dc49fc127f6c0060e88ba32efa8a863b5ed2aa8d6b9e6fdf45 | Rust | 3,435 | 118 | //! Version information for coglet.
/// Coglet version from Cargo.toml
pub const COGLET_VERSION: &str = env!("CARGO_PKG_VERSION");
/// Version information for the runtime.
#[derive(Debug, Clone, serde::Serialize)]
pub struct VersionInfo {
/// Coglet runtime version.
pub coglet: &'static str,
/// Git SHA (... |
71656c0f66969bd4383ef37eaab978f8d9d10b7463981c2c42d634e35a3b679b | Rust | 3,448 | 84 | //! Functional (not byte-identity) test: a scaffold-heavy genome.
//!
//! Perl `bismark2bedGraph`'s default mode opens **one temp filehandle per
//! chromosome** (`:274-283`), so a genome with thousands of scaffolds exceeds
//! `ulimit -n` (~1024) and Perl dies — which is the whole reason Perl's
//! `--gazillion` mode ... |
6f62c8db71df1a2b9ee260a8ba982f42bb92caa7bf03b8607903f51d56f1f718 | Rust | 3,453 | 96 | //! Sentry error reporting integration.
//!
//! Initializes Sentry when `SENTRY_DSN` is present in the environment.
//! When no DSN is configured, the SDK creates a disabled (no-op) client
//! with zero runtime overhead.
use tracing::info;
/// Guard returned by [`init_sentry`]. Must be held for the lifetime of the
//... |
659db7bda0cf38d5e29cfbca3532a40a50815d97c3351fd41ff4b036ff77ffdb | Rust | 3,591 | 124 | //! HTTP server implementation.
use std::net::SocketAddr;
use std::sync::Arc;
use tokio::net::TcpListener;
use tokio::sync::watch;
use tracing::info;
use crate::service::PredictionService;
use super::routes::routes;
#[derive(Debug, Clone)]
pub struct ServerConfig {
pub host: String,
pub port: u16,
/// ... |
702fc4217693aeddc4d8277b613a78f7e42dc8f53fc5f2ce252bd46ca677dfdf | Rust | 3,610 | 89 | //! `bismark-genome-preparation` — Rust port of the Perl `bismark_genome_preparation`.
//!
//! Reads a genome directory of FASTA file(s) and writes two in-silico
//! bisulfite-converted references — a **C→T-converted** (top-strand) copy and a
//! **G→A-converted** (bottom-strand) copy — under
//! `<genome>/Bisulfite_Ge... |
76c8c14666a913b6ec9a7b70228a1f06ab9c17e1ddd949ffabe73af0e2de83a0 | Rust | 3,615 | 109 | use std::sync::Arc;
use brush_render::Backend;
use burn::tensor::Tensor;
use burn_wgpu::{JitTensor, WgpuRuntime};
use egui::TextureId;
use wgpu::ImageDataLayout;
fn copy_buffer_to_texture(
img: JitTensor<WgpuRuntime, f32>,
texture: &wgpu::Texture,
encoder: &mut wgpu::CommandEncoder,
) {
let [height, w... |
e7d6ba70f2e8bb98680d479909fca82d85fddefaab36220ef6e12a80f22acbaf | Rust | 3,616 | 133 | //! Predictor traits and prediction lifecycle types.
use std::collections::HashMap;
use std::time::{Duration, Instant};
pub use crate::prediction::{CancellationToken, PredictionOutput};
/// Result of a completed prediction.
#[derive(Debug, Clone)]
pub struct PredictionResult {
pub output: PredictionOutput,
p... |
92e55f3228a44a9b3df58c52f129a090685ea7ce9ec68fedd36fea854b8d2902 | Rust | 3,617 | 91 | //! Cancellation support for predictions.
//!
//! Sync predictors use `PyThreadState_SetAsyncExc` to inject a
//! `CancelationException` (a `BaseException` subclass) into the Python
//! thread running `predict()`.
//!
//! Async predictors use asyncio task cancellation:
//! - Store task reference when prediction starts
... |
c7fa86afe4354dac2477864d3296d2bbdcdb334605243fa574693f066535e0ed | Rust | 3,667 | 86 | //! Typed errors for `bismark-summary`.
//!
//! All variants are produced at the orchestration / pipeline layer. The
//! binary's `main` maps any error to a nonzero exit code (the value is not
//! byte-gated; STDERR text is informational). Mirrors the `bismark-dedup`
//! `error.rs` shape.
use std::path::PathBuf;
/// ... |
ccffb0e6dc1038c42c5c2750631bef9c072ad1da4315aac738da1801ab358462 | Rust | 3,773 | 145 | //! Binary-level behaviors: exit codes, output naming, `-o`, and error paths
//! (PLAN D4 / §6.1). These do not need Perl.
use std::path::Path;
use assert_cmd::Command;
use tempfile::tempdir;
fn bin() -> Command {
Command::cargo_bin("bismark2report").unwrap()
}
fn minimal_pe_report() -> Vec<u8> {
std::fs::r... |
35068ba11fc3e4e47305ceae80840751ddf71fe5b396d6aa1ac6929e7f428e20 | Rust | 3,841 | 97 | //! HTML `{{report_timestamp}}` formatting.
//!
//! Perl uses scalar `localtime` (`bismark2summary:488`), a C `ctime` string:
//! `"Www Mmm <space-padded D> HH:MM:SS YYYY"` (e.g. `"Mon Jun 1 09:07:00
//! 2026"` — note the two spaces before a single-digit day-of-month).
//!
//! **Deliberate deviation (documented):** th... |
34dec8e21a209c05dfa481f1a864a76dec546748ae4bfaf2dada56b927401b25 | Rust | 3,875 | 112 | //! Bismark coverage-file (`*.bismark.cov[.gz]`) reading + line parsing.
//!
//! Mirrors Perl `generate_genome_wide_cytosine_report:184-209`: gz-aware open,
//! tab-split, **column 4 (percentage) and column 3 (end) discarded**, 1-based
//! `start` as the lookup key. Parse policy folded from Phase-B review (B-I1/2/3):
/... |
7f1f45c7fbd079386031340021be20b14f24f6f267c9311b497520ebeb9af086 | Rust | 3,963 | 94 | //! Typed errors for `bismark-bedgraph`.
//!
//! Variants are produced at CLI-validation and pipeline boundaries.
//! Messages mirror Perl `bismark2bedGraph` v0.25.1 where a user-facing
//! string exists (cited by Perl line number). The binary's `main` maps
//! any [`BismarkBedgraphError`] to exit code 1 (clap parse er... |
934a9ec591d394f151cb6867d69a6b155f72d437102d66ce4fc18f0b32c8f636 | Rust | 3,979 | 103 | // Autogenerated by brush-wgsl from source wgsl files. Do not edit.
#![allow(dead_code, unused_mut, clippy::all)]
fn create_composer() -> naga_oil::compose::Composer {
let mut composer = naga_oil::compose::Composer::default().with_capabilities(
naga::valid::Capabilities::SUBGROUP |
naga::val... |
2a9dcf564994c3427106ec2f6e3487cc74bf01a24be1ad0b23ac10487faaa8eb | Rust | 3,988 | 115 | //! methylseq CLI-surface conformance — `BISMARK_COVERAGE2CYTOSINE`
//! (nf-core/methylseq **4.2.0**).
//!
//! Asserts the Rust `coverage2cytosine` CLI accepts every command methylseq's
//! c2c module emits. See `plans/06122026_methylseq-cli-conformance/`.
//!
//! **Command template** (`modules/nf-core/bismark/coverage... |
0346f24f65aaefc0c9bf922f2b8e65f5019fde67ab4fe5ac9658bc7fa00b0469 | Rust | 3,991 | 115 | //! Custom tracing layer for worker subprocess.
//!
//! Ships structured tracing events over IPC to orchestrator, preserving target and level.
//! Optionally writes to fd 101 for direct debugging (controlled by RUST_WORKER_DIRECT_LOG=1).
use std::io::Write;
use std::sync::{Arc, Mutex};
use tokio::sync::mpsc;
use trac... |
57e8c630ea97f3ce67c249a433d567a897df46a2e3fadc1ea934d1e11114fb26 | Rust | 4,015 | 102 | //! methylseq CLI-surface conformance — `BISMARK_DEDUPLICATE` (nf-core/methylseq **4.2.0**).
//!
//! Asserts the Rust `deduplicate_bismark` CLI accepts every command methylseq's
//! `BISMARK_DEDUPLICATE` module emits. See `plans/06122026_methylseq-cli-conformance/`.
//!
//! **Command template** (`modules/nf-core/bismar... |
67d7ed034ec680f9ef277ef904a4ae0db8418fe092959630d5421ed78373d94c | Rust | 4,018 | 81 | //! Shared build-time version/provenance for the Bismark Rust suite.
//!
//! The **suite version** (single source: `rust/VERSION` or `$BISMARK_SUITE_VERSION`),
//! the git short-hash, and a reproducible build timestamp are captured at build
//! time by `build.rs`. Every Bismark Rust binary reports the *suite* version v... |
08ae8db848765843112338848b0c8178f2d010195a6b8d6b671b2960e9ea919f | Rust | 4,135 | 117 | //! The always-on cytosine-context summary (`*.cytosine_context_summary.txt`).
//!
//! Mirrors Perl `reset_context_summary` (`:1961-1975`), `context_reporting`
//! (`:1977-1988`), and `print_context_summary` (`:63-78`): a 64-cell grid of
//! the 16 `C{A,C,G,T}{A,C,G,T}` trinucleotides × 4 upstream bases `{A,C,G,T}`,
//... |
1eed75f46b2fa0f9e7adc60d316d6a512bd49b064da2c72e9cb018affe382b42 | Rust | 4,263 | 113 | //! Top-level orchestration: Step I (folders + discovery + early aligner-path
//! validation) → Step II (conversion) → Step III (indexing) → Step IV (opt
//! combined genome).
use crate::genome_prep::cli::{Aligner, Cli};
use crate::genome_prep::error::GenomePrepError;
use crate::genome_prep::logging::Logger;
use crate... |
1f65051a36c5bbde6ebfdb010c74a197d9c4de8ab6e7e7d05d862456239a3f8a | Rust | 4,296 | 124 | //! Real-data byte-identity gate (Phase 6, `#[ignore]`).
//!
//! Runs Perl `bismark2bedGraph` v0.25.1 and `bismark2bedGraph_rs` on the
//! SAME methylation-extractor call files in the SAME argv order, and asserts
//! their **decompressed** bedGraph + coverage are byte-identical (SPEC §1.1
//! D1). This is the genuinely... |
39fc729518f5123f638ab5f9704c467c07e91adf56a1491d37b737cb78118815 | Rust | 4,297 | 112 | //! Faithful reimplementation of C `printf("%.15g", x)` — the format Perl
//! uses for default scalar (NV) stringification.
//!
//! In `bismark2summary` this powers the **unmethylated** percentage arrays
//! (SPEC §2.9a): `$p_*_unmeth = 100 - $p_*_meth`, where `$p_*_meth` is an
//! already-rounded `%.2f` string. Perl n... |
f83185f87cf04d59cdf88b7fd8fc7dd60582406e091a87bc2404d60572cc8cd4 | Rust | 4,323 | 117 | //! Phase A sanity test.
//!
//! Spawns the `deduplicate_bismark` binary with `--version` and asserts the
//! output matches the uniform suite provenance regex. This is the minimum bar for
//! Phase A: the binary builds, runs, and emits a recognisable identity string.
use assert_cmd::Command;
use predicates::prelude::... |
3ad093b96c07311e223f7493dbd7187db8cbd0a15a1968c32239317d59534603 | Rust | 4,395 | 110 | //! Deduplication report parser + fill (SPEC §2.7b).
use crate::report::reports::{before_first_ws, field1_owned, join_with, report_lines};
use crate::report::template::subst_all;
/// Captured deduplication fields.
#[derive(Debug, Default)]
pub struct Dedup {
pub total_seqs: Option<Vec<u8>>,
pub dups: Option<V... |
331b270c798efe3738c8d31f8526d81751f0fd767f2575185230a929b5f9cf61 | Rust | 4,464 | 124 | //! `bismark-bedgraph` — Rust port of Bismark Perl's `bismark2bedGraph`.
//!
//! Consumes the methylation extractor's per-context call files
//! (`CpG_OT_*`, `CpG_OB_*`, … and the CHG/CHH equivalents with `--CX`) and
//! emits a sorted, gzip-compressed bedGraph + coverage file. Installed as
//! `bismark2bedGraph` durin... |
8827db997a8c337df6e5005506a79570eeb5daa73e9d8f3b0cddd08798b965ed | Rust | 4,691 | 150 | //! Build script for coglet-python.
//!
//! Captures build metadata and converts semver to PEP 440 for Python compatibility.
use std::process::Command;
fn main() {
// Convert CARGO_PKG_VERSION (semver) to PEP 440
let version = env!("CARGO_PKG_VERSION");
let pep440 = semver_to_pep440(version);
println!... |
0077b8e4dcc7431d0894e22fc994cf9291c708988af56f4b2d44973c895a826a | Rust | 4,747 | 143 | //! Output-filename derivation matching Perl `methylation_consistency`.
//!
//! Perl line 186: `my $file_root = $file; $file_root =~ s/\.bam$//;`. That
//! is the *entire* derivation — strip a **single trailing `.bam`** and keep
//! everything else (including the full directory prefix) verbatim. Outputs
//! are written... |
95ca3a70f0da4042de3ecc1c79102d81f22443ee7f6f064cdaed42b252bb9183 | Rust | 4,834 | 116 | //! Typed errors for `filter_non_conversion`.
//!
//! Display strings echo the Perl `filter_non_conversion` `die`/`warn`
//! messages where practical. These are surfaced on STDERR (not part of the
//! byte-identity gate, which covers the BAM bodies + report file), but
//! keeping them faithful eases cross-checking agai... |
6f52ad6db26f9b815b6c8c396465a8a6329b4f8eba74075bebca049414027ef2 | Rust | 4,924 | 120 | //! `bismark-coverage2cytosine` — Rust port of Bismark Perl's `coverage2cytosine`.
//!
//! Reads a Bismark coverage file (`*.bismark.cov[.gz]`) + the genome FASTA and
//! emits a genome-wide per-cytosine report (CpG by default; all-context with
//! `--CX`). This crate is the second producer (after `bismark-bedgraph`,
/... |
5e768b49816588764ec7f59fe8d1c9b86451a155030ff06472c5318ed84ef316 | Rust | 4,937 | 176 | //! Health status types for coglet runtime.
use serde::{Deserialize, Serialize};
/// Health status of the coglet runtime.
#[derive(Debug, Clone, Copy, Default, PartialEq, Eq, Serialize, Deserialize)]
#[serde(rename_all = "SCREAMING_SNAKE_CASE")]
pub enum Health {
/// Just started, status unknown
#[default]
... |
7fa96e26c2dae66f07e2236e456fb0530c19af25b75cd5bc2bf853ef2e41689e | Rust | 4,958 | 120 | //! Embedded `plotly/` assets + the `read_report_template` line normalizer.
//!
//! The HTML template itself is the inline Perl heredoc, extracted verbatim
//! into `summary_template.html` (see [`crate::summary::html::TEMPLATE`]). The three
//! companion assets — `plot.ly` (~3 MB), `bismark.logo`, `bioinf.logo` — are
/... |
7c5a1436d9ffae9972bf9e0ed5724026be139b08ea39c00550b658838cedab13 | Rust | 5,068 | 135 | //! `bismark-filter-nonconversion` — Rust port of Bismark Perl's
//! `filter_non_conversion` script.
//!
//! Reads a Bismark BAM, walks each read's `XM:Z:` methylation-call string,
//! and removes reads (SE) / read-pairs (PE) with too much **non-CpG**
//! methylation (apparent incomplete bisulfite conversion). A verbat... |
090e356058a97fdf286775daac904c82f0971100ee0afeb0ca215e9cd56be864 | Rust | 5,161 | 148 | //! Report parsers. Each submodule exposes a pure `parse(&[u8]) -> Captured` plus
//! a `fill(doc, &Captured) -> doc`. The split keeps parsing unit-testable
//! without any template, and concentrates Perl's **sequential** whole-document
//! substitution ORDER in `fill` (SPEC §8: a later `{{name}}` replace can legally
/... |
27d43d6e78e6cac16efa1ad60070d520e3d7ec44d9bab9189d58744fa9b70b3d | Rust | 5,230 | 125 | //! `bismark-nome-filtering` — Rust port of Bismark Perl's **standalone**
//! `NOMe_filtering` (v0.25.1). A per-read NOMe-Seq classifier that consumes the
//! methylation extractor's `--yacht` output and emits a per-read CG/GC
//! methylation tally; byte-identical to Perl v0.25.1.
//!
//! ⚠️ This is the standalone tool... |
5953242545d3e7d5c5a9b3cc942c836e5908679f91faacd906d716134f78a88b | Rust | 5,265 | 166 | //! Real-data byte-identity gate for `filter_non_conversion_rs`.
//!
//! `#[ignore]`d + env-gated: runs the REAL Perl `filter_non_conversion`
//! v0.25.1 AND the Rust binary on a real Bismark BAM, then asserts the
//! decompressed kept/removed bodies (`samtools view`) and the report
//! (timing-line-normalized) are byt... |
62f63e1123403eccb056c032412c32f69b27d3d6fdffe8aabefb2ea7787b7e5e | Rust | 5,282 | 131 | //! `bismark-bam2nuc` — Rust port of Bismark Perl's `bam2nuc`.
//!
//! Computes the **mono- and di-nucleotide coverage** of a Bismark alignment as
//! a QC metric: for every read with a clean (no `I/D/S/N`) CIGAR it tallies the
//! **genomic** sequence at the read's mapped span (NOT the read's own bases),
//! reverse-c... |
936fc236c1b94808f7936514d5e491d56448658b59614b7493e5c90a5faeef93 | Rust | 5,299 | 151 | //! CLI-behavior tests for the flags that don't shape the *content* of the
//! data streams (and so aren't covered by the byte-identity cells):
//! `--dir` (output placement + directory creation), the accepted-but-ignored
//! no-op flags (`--remove_spaces`, `--counts`, `--buffer_size`,
//! `--ample_memory`, `--gazillio... |
98575dfb5aebd55d9cdf8460bfbbec821490730cf5cce01bb18a395e469e9926 | Rust | 5,302 | 136 | //! The four embedded Plotly assets + the faithful `read_report_template`
//! line-normalizer (SPEC §2.6 / §8.2).
//!
//! Embedding strategy: `include_str!` from the crate-local `assets/` directory
//! (VENDORED copies of the repo `plotly/` files) so the crate is SELF-CONTAINED
//! and publishable to crates.io — a `.cr... |
b1c08fffed9d7a2aec74f792fcb7e93f1c391d8b30d188aad3d9ae9118e77a01 | Rust | 5,310 | 161 | use crate::camera::Camera;
use crate::safetensor_utils::safetensor_to_burn;
use crate::{render::num_sh_coeffs, Backend};
use burn::tensor::Distribution;
use burn::tensor::Tensor;
use burn::{
module::{Module, Param, ParamId},
tensor::Device,
};
use safetensors::SafeTensors;
#[derive(Module, Debug)]
pub struct S... |
6d2b50dde29b4c4bbe58c4bc5bf6950a66ad41bc43cd1aaaac828a99ffee0bb7 | Rust | 5,473 | 164 | use std::io::Cursor;
use std::io::Read;
use std::path::Path;
use anyhow::Context;
use anyhow::Result;
use brush_render::camera;
use brush_render::camera::Camera;
use brush_train::scene::SceneView;
use crate::clamp_img_to_max_size;
use crate::normalized_path_string;
// TODO: This could be simplified with some serde-... |
b24dddc482d16a717e828cb730ec97c9ae4b9878bf6c9a375826a6414153228b | Rust | 5,583 | 137 | //! Phase 3 — multicall dispatch tests (DECISIONS D2/D3/D4/D7).
//!
//! The classic-name byte-identity tests live in each tool's own `*_…` test files
//! (invoked via the classic `[[bin]]` → `argv[0]` alias → unchanged `run_main`).
//! These cover the NEW `bismark <subcommand>` / bare-`bismark` dispatch surface.
//! Th... |
c0f37422a6b62df4e5dd72fd98156a6099fc9b3555f1925d9806f2206ee3cf68 | Rust | 5,585 | 142 | //! `bismark-report` — Rust port of the Perl `bismark2report`.
//!
//! Reads a Bismark **alignment** report (mandatory) plus up to four optional
//! companion reports — **deduplication**, methylation-extractor **splitting**,
//! **M-bias**, and **nucleotide coverage** — and fills a single self-contained
//! HTML templa... |
624815bcae1f93f61806316e0f77596e691ddeea24bb6bc63afeeb8692ab2ace | Rust | 5,691 | 178 | //! Framed codec for worker communication.
//!
//! Uses LengthDelimitedCodec for framing + serde_json for serialization.
//! Works over any AsyncRead/AsyncWrite (pipes, sockets, etc).
use std::io;
use std::marker::PhantomData;
use serde::{Serialize, de::DeserializeOwned};
use tokio_util::bytes::{Bytes, BytesMut};
use... |
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