sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6e9b0037cbb91b2d8bc7551219713422d6cc46ff15f4d0d91781589126d0b788 | Rust | 15,792 | 366 | //! HTML report assembly — the string-templating engine.
//!
//! Reproduces Perl `bismark2summary:1376-1719` mutation-for-mutation, in
//! order (§2.9). The two riskiest behaviors are pinned here:
//!
//! - **Section deletion uses TWO independent predicates** (§2.9 ⚠ box,
//! Reviewer A C2): the *numbers* sections ke... |
2dd992318f9f76d84e34817288ff6eb6b4e207c8660aa33e5d02cc9c1ce9ce8e | Rust | 16,126 | 532 | //! Permit pool implementation with typestate for compile-time state transition safety.
//!
//! Slot poisoning is a pool-level property: a poisoned slot is permanently removed
//! from the pool regardless of whether a prediction was active on it.
use std::sync::Arc;
use std::sync::Mutex as StdMutex;
use std::sync::ato... |
9bcb3bf1f16bfc7e7ddbf035e3c8d0819a007e428dd4089bc43a89da1a7f16bf | Rust | 16,288 | 426 | //! Whole-genome FASTA reader for Bismark genome folders, faithful to Perl
//! `read_genome_into_memory` + `extract_chromosome_name` (as used by both
//! `coverage2cytosine` and the standalone `NOMe_filtering`).
//!
//! This is a **shared, tier-parameterized** promotion of the reader that
//! `bismark-coverage2cytosine... |
933824f07e99bc43ffa10a933880abefb64dd9e32210fc3f5fe48c2746fbbb4b | Rust | 16,531 | 431 | //! Command-line interface for `deduplicate_bismark`.
//!
//! [`Cli`] is the clap-derived parser. [`Cli::validate`] resolves the
//! parsed arguments into a [`ResolvedConfig`] and rejects unsupported /
//! conflicting flag combinations:
//!
//! - `--barcode` / `--umi` → engages UMI-aware dedup (v1.2+; tail-of-qname
//!... |
28ffc1cf2f4bdcb0a51e8e1cff57bc55b035eae3850732d69f5953fcefba905a | Rust | 16,605 | 453 | //! Phase B byte-identity golden tests + streaming edge cases.
//!
//! Goldens in `tests/data/coverage2cytosine/phase_b/*.golden` are generated by
//! `tests/data/coverage2cytosine/phase_b/generate_goldens.sh` from the repo's Perl
//! `coverage2cytosine` v0.25.1 (self-contained Perl). The Rust binary's output
//! must ... |
017305d5001ed3f9b30ffa735ac36dd68dcd39c9342101611d45023e2e262380 | Rust | 16,629 | 448 | //! Report parsers and the per-sample metric record.
//!
//! Mirrors Perl `bismark2summary:248-385`. Every field is a `String` that
//! starts empty (`''` in Perl) so the `.txt` reproduces Perl's "not found =
//! empty cell" semantics byte-for-byte (§2.6). Parsing is **last-match-wins**
//! (scan every line; a later ma... |
26455d75bb0f007a5171a853cf1522ed2d3f20509ab85243c5506c52a9ca953a | Rust | 16,678 | 548 | //! Perl-oracle byte-identity gate (the primary acceptance test).
//!
//! For each fixture shape, build a report set in a temp dir, run BOTH the
//! Perl `bismark2summary` (v0.25.1) and the Rust `bismark2summary_rs`, and
//! assert:
//! - `.txt` is **byte-for-byte identical**;
//! - `.html` is **byte-identical after no... |
126935ec6f6949a324a277212058a9f02026845d6f00a12cc9ce5a8dcd02cd51 | Rust | 17,079 | 420 | //! MAPQ computation — a verbatim port of Perl `calc_mapq` (3923–4186), both the
//! **end-to-end** and **`--local`** branches (the local ladder, `4082-4178`, ships for
//! Bowtie 2 since #981 and HISAT2 since the HISAT2-`--local` work).
//!
//! The returned MAPQ integers are **byte-identity-critical** — they land in t... |
cbeacf96a65bd6c0902f2e2e0fee7e9fe44281c11f1a1382838eecde78d20c2e | Rust | 17,223 | 502 | //! The byte-identity core: bisulfite conversion of FASTA sequences.
//!
//! Faithful to Perl `process_sequence_files` (lines 360–516). The transform
//! operates on **raw line bytes including the terminator**, so CRLF stays CRLF
//! and a final line without a newline keeps none — never trim-and-re-emit.
//!
//! Per se... |
c20eca0133503b34d3b3d7c25167f8e9d20e27a0b68b44d5828beaf229229551 | Rust | 17,759 | 461 | //! `--genomic_composition`: the mono- + di-nucleotide frequency table
//! `<genome>/genomic_nucleotide_frequencies.txt`, **byte-identical** to Perl
//! `bismark_genome_preparation`'s `get_genomic_frequencies` / `process_sequence`
//! / `read_genome_into_memory` (lines 518–570, 665–751).
//!
//! **This is NOT the conve... |
2a1758a93949cbe7f0519634e3dfde1f80473d1fb2d9bedbe21e817bdc7eb681 | Rust | 17,990 | 546 | use std::sync::atomic::{AtomicBool, Ordering};
use std::time::Duration;
use std::collections::HashMap;
use axum::http::HeaderMap;
use opentelemetry::propagation::{Extractor, Injector, TextMapPropagator as _};
use opentelemetry::trace::{TraceContextExt as _, TracerProvider as _};
use opentelemetry::{Context, KeyValue}... |
fb42011b8368ed9cff1adc088cab09f194b5c70ad1d83199e761b24df2ff92f2 | Rust | 18,558 | 415 | //! Methylation-call classification + per-record extraction kernel.
//!
//! Phase B (rev 1): delegates the CIGAR walk + `-`-strand orientation
//! correction to `bismark-io 1.0.0-beta.6`'s `BismarkRecord::iter_aligned`.
//! Per SPEC §7.1 rev 2 note, the kernel is a thin filter over that iterator.
use crate::io::Bismar... |
b9766da29d7068ce41ab66d6874dccc2a7044fa37b2b6aa145561897729836a5 | Rust | 18,704 | 468 | //! Per-read genomic-sequence counting.
//!
//! For each read with a clean CIGAR (no `I/D/S/N`), bam2nuc takes the GENOMIC
//! sequence at the read's mapped span — `substr(chr, POS-1, len(SEQ))`, NOT the
//! read's own bases (Perl `generate_nucleotide_report` `:109-142`) — reverse-
//! complements it for reverse-strand... |
571c558dc944520a1ee652067c1ee472df6be3bfe6b6f3e1905a571df3aba527 | Rust | 18,786 | 554 | use anyhow::Context;
use async_channel::{Receiver, Sender, TryRecvError, TrySendError};
use brush_dataset::scene_batch::SceneLoader;
use brush_render::{camera::Camera, gaussian_splats::Splats};
use burn::tensor::ElementConversion;
use burn::{backend::Autodiff, module::AutodiffModule};
use burn_wgpu::{JitBackend, Runtim... |
e674ef12b147182950ee6d71ec257dd332dae9c71e6ef95ce65399255626091a | Rust | 18,790 | 478 | //! `--drach` / `--m6A` — the standalone DRACH-motif (m6A) report.
//!
//! Mirrors Perl `generate_DRACH_report:1075-1383`: a **standalone early-exit
//! mode** (invoked from `lib::run` *instead of* the normal cytosine report —
//! Perl `:38-42`). It re-reads the coverage file, buffers one chromosome at a
//! time, scan... |
22fbae6add2a9324ac1927fdcde200ae6764809e9ca95913232cf9b008f42bfe | Rust | 18,935 | 464 | //! `bismark-dedup` — Rust port of Bismark Perl's `deduplicate_bismark` script.
//!
//! This crate is the first downstream binary of the Bismark Rust rewrite, built
//! on top of [`bismark_io`] for all BAM/SAM/CRAM I/O. The binary is installed as
//! `deduplicate_bismark` during the v0.26 → v1.0 coexistence period.
//!... |
e324026d7515e2be399698a4f4351936dd24a24cdbfc3795e27ba2341c7122f1 | Rust | 19,115 | 547 | use anyhow::Result;
use brush_render::gaussian_splats::Splats;
use brush_render::{AutodiffBackend, Backend, RenderAux};
use burn::lr_scheduler::linear::{LinearLrScheduler, LinearLrSchedulerConfig};
use burn::lr_scheduler::LrScheduler;
use burn::nn::loss::HuberLossConfig;
use burn::optim::adaptor::OptimizerAdaptor;
use ... |
035817124bfce1ffd32afb7ec05798668e27399e032a76d2e2dc66627d92063e | Rust | 19,178 | 574 | //! Output processing for prediction results.
//!
//! Converts Python prediction output to JSON-serializable format:
//! - Pydantic models -> dict (via model_dump() / dict())
//! - Dataclasses -> dict (via dataclasses.asdict())
//! - Enums -> .value
//! - datetime -> .isoformat()
//! - PathLike -> base64 data URL
//! -... |
a6ac700310a23a5947766a8cda7328e2b280d23248df58ba98c9f358f65f9f8b | Rust | 19,360 | 468 | //! Real-data byte-identity gate for `deduplicate_bismark_rs`.
//!
//! This is **the headline correctness test** for `bismark-dedup` v1.0:
//! given a real Bismark-aligned BAM, the Rust port must produce a
//! deduplicated BAM with the **same set of retained qnames** as
//! Bismark Perl v0.25.1, AND a deduplication rep... |
1988628912dac4eaeeb267b4fe17a26553d7af3220eaafe1575222bee3973462 | Rust | 19,361 | 417 | //! Aggregated extraction state — file handles, M-bias counters, splitting
//! report.
//!
//! Owned by the SE/PE pipeline; created at `extract_se` entry and dropped
//! at exit. Per SPEC §6.1 + §6.3: per-call helpers receive `&mut ExtractState`
//! rather than 14 positional args.
use std::path::Path;
use crate::extr... |
7f13232f16608991f76a0718ab8ce0556a837ff0973c6e00d77d7d428e723010 | Rust | 19,539 | 420 | //! In-memory aggregation of methylation calls into per-position counts,
//! plus chromosome ordering — the most byte-identity-load-bearing module
//! (SPEC §2.1, decision D3).
//!
//! Replaces Perl's pre-split-to-temp-files + per-file `sort -k4,4n` +
//! sequential tally (`bismark2bedGraph:160-506`) with a direct in-m... |
ddeab5fd3a683c1103d152a8264ae075251a6fc6525a42cca7b5e1cb1c77f90d | Rust | 19,575 | 623 | //! Phase E unit tests — output-mode dispatch + gzip + yacht row format.
//!
//! Kernel `mbias_only_silence` tests live in `se_phase_b.rs` where the
//! synthetic-record helpers are defined; this file is pure mode/key/yacht
//! testing that needs no synthetic BAM records.
#![allow(non_snake_case)]
use std::fs;
use st... |
da5666ff9f87098363b6e3091ca509c379d94df8e82ca175f3e193d38e235e97 | Rust | 19,602 | 506 | //! End-to-end tests for v1.x: multiple input files + single-end
//! coordinate-sorted input.
//!
//! Builds synthetic BAMs in-test (no Perl/samtools toolchain), runs the
//! `bismark_methylation_extractor_rs` binary, and asserts the v1.x contract:
//!
//! - SE coordinate-sorted input is ACCEPTED (explicit `--single-en... |
4afd4b7c1ae2a5cb82b8e51081821a9a640fed07f1e2b5fdb79ee074784b0081 | Rust | 20,601 | 580 | //! Integration tests for `bismark_genome_preparation_rs`.
//!
//! - Binary end-to-end with a **fake indexer** (`BISMARK_BIN`) so the run
//! completes without a real `bowtie2-build` installed; asserts the converted
//! CT/GA FASTA bytes.
//! - **Perl oracle**: runs the actual `bismark_genome_preparation` and the R... |
8a0c1373b7519aadce16f4858973717615acc6367e71191a98fefeac0f16afb7 | Rust | 20,679 | 567 | //! Core dedup primitives.
//!
//! Pure logic, no I/O. The two types here are:
//!
//! - [`DedupKey`] — the value used to detect duplicates. Single key shape
//! serves both single-end and paired-end (SE uses `end == start`), and is
//! used for BOTH the seen-set and the positions-counter. That last point
//! mat... |
bd4c76e3209a3b3031bdecb120cd7bb49eee5a6814911e75c73261c849d91fbd | Rust | 20,931 | 481 | //! Phase D unit tests — M-bias.txt writer, filename derivation,
//! MbiasTable::max_position, SE-vs-PE section ordering, finalize ordering.
//!
//! Test names mirror plan §7.1's labels. End-to-end smoke that runs the
//! binary on real BAMs lives at `tests/mbias_writer_phase_d_smoke.rs`.
#![allow(non_snake_case)]
us... |
04f099eb48b3e315fd1c7094553217eb5c51416270c2c29f23a10018bfa5e181 | Rust | 20,990 | 558 | //! The GpC-context report (`--gc`/`--gc_context`) + NOMe-Seq GpC filtering.
//!
//! Mirrors Perl `generate_GC_context_report:751-1073`: a SECOND genome walk —
//! run after the core report + context summary — that re-reads the same
//! coverage file and, for every `GC` dinucleotide of each *covered* chromosome,
//! em... |
8b05499a9bf8c039cfc4fadf1537fd189d7c4a6586486ca8abaae0aa34208b1c | Rust | 21,017 | 642 | //! Webhook sender for async predictions.
//!
//! Implements the cog webhook protocol:
//! - Throttling (default 500ms between non-terminal updates)
//! - Terminal webhooks retried with exponential backoff
//! - WEBHOOK_AUTH_TOKEN bearer authentication
//! - Events filtering (start, output, logs, completed)
//!
//! # P... |
b31d20003a1f8f78a53be44488c269691a9c893ae98069c0d5eb085cf0ed7700 | Rust | 22,587 | 633 | //! Input validation against the OpenAPI schema.
//!
//! Validates prediction inputs before dispatching to the Python worker.
//! Strips unknown fields silently and catches missing required fields
//! with clear error messages (matching the format users expect from pydantic).
use std::collections::HashSet;
use serde_... |
bc238f0240b95edd8ee32c8663ad337191d35f12b7738b9d4691e108c57498db | Rust | 22,588 | 651 | //! Phase E end-to-end smoke tests.
//!
//! Spawn the `bismark_methylation_extractor_rs` binary with each of the
//! Phase E output modes (`--comprehensive`, `--merge_non_CpG`, both,
//! `--yacht`, `--mbias_only`) and `--gzip`, on a synthetic SE-directional
//! BAM, and assert:
//! - exit code 0,
//! - the expected... |
73806ff8d28dd47038726c76e79082b2a392953c229d00f13d6f1ee97d3fa03d | Rust | 22,993 | 641 | //! #1025 Phase 2, integration tests for the BINSEQ (`.vbq`) → temp-FASTQ transcode.
//!
//! Builds real (tiny) VBQ files with the `binseq` writer (re-exported by the lib under
//! the `binseq-input` feature), then checks `transcode_binseq_to_fastq_se`/`_pe` produce
//! the expected `bqtools decode`-equivalent FASTQ, e... |
b3709d8fad52953d36ae4c8b1036f360de3e1ea88e457ec49d99414bc272fbc3 | Rust | 23,058 | 647 | //! Log routing via prediction_id ContextVar.
//!
//! Architecture:
//! - Rust owns a ContextVar `_coglet_prediction_id` that holds the current prediction ID
//! - Rust maintains a registry mapping prediction_id -> SlotSender
//! - SlotLogWriter reads the ContextVar to route logs to the correct sender
//!
//! This desi... |
2823303e35632f189b37fb0e690b3446bb199a214b615cd33be3ac4f72ea0015 | Rust | 23,248 | 434 | //! Command-line surface (clap derive).
//!
//! Declares the **full** Bismark option set (the `GetOptions` block, Perl
//! 7317–7382) so `--help` and `@PG` argv fidelity are complete, but only the
//! **v1 spine** (Bowtie2 + FastQ + directional + SE) is *wired* downstream by
//! [`crate::aligner::config`]. Options excl... |
15f05d79d5b4aefdda03c8b0ea024c2d172c59b4051242630cfb77983ec783cf | Rust | 23,550 | 774 | //! Wire protocol types for parent-worker communication.
//!
//! Two channels:
//! - **Control channel** (stdin/stdout): Init, Cancel, Shutdown, Ready, Idle
//! - **Slot sockets**: Prediction data, streaming logs (per-slot to avoid HOL blocking)
use std::collections::HashMap;
use serde::{Deserialize, Serialize};
use... |
43569c9dc14681f2b4d6b1d357e8ada49ca477b338fc9da7a0fba24885767113 | Rust | 23,716 | 614 | //! The per-read NOMe-Seq filtering pipeline — the byte-identity crux.
//!
//! Ported from Perl `NOMe_filtering` `per_read_filtering:48-230` (the streaming
//! loop + the in-loop/EOF flush) and `cytosine_lookup:242-391` (the C/G walk +
//! NOMe filter + tally). The output is the always-gzipped `.manOwar.txt.gz`
//! per... |
d988eb8f42d9f7f52df224c1f274f49b354cd4820430971f7ecf90549dda82c2 | Rust | 24,307 | 697 | //! coglet-python: PyO3 bindings for coglet.
mod audit;
mod cancel;
mod input;
mod log_writer;
mod metric_scope;
mod output;
mod predictor;
mod sentry_integration;
mod worker_bridge;
use std::sync::Arc;
use std::sync::atomic::{AtomicBool, Ordering};
use pyo3::prelude::*;
use pyo3_stub_gen::derive::*;
use tracing::{I... |
635040fa4d399758e6c36b19dea77c8dfadf39a9ebb28dc5b52d3181dfd48fbc | Rust | 25,417 | 748 | //! Command-line interface for `coverage2cytosine`.
//!
//! [`Cli`] is the clap-derived parser; [`Cli::validate`] resolves it into a
//! [`ResolvedConfig`], reproducing every Perl `process_commandline`
//! (`coverage2cytosine:1990-2197`) validation rule. All v1.x niche flags are
//! now supported — `--gc`/`--nome-seq` ... |
47a0c49049164adcae3c4e13ae00a66b71961b7088e2eae1df331509b6f679d9 | Rust | 25,622 | 611 | //! Genome folder + bisulfite-index + raw-FASTA discovery.
//!
//! Mirrors Perl `bismark` 7604–7800 / `read_genome_into_memory` 5031–50:
//! - the genome folder is made **absolute** (Perl `chdir`+`getcwd`);
//! - the Bowtie 2 small index (`BS_CT.{1,2,3,4,rev.1,rev.2}.bt2`) is required,
//! with a **large** (`.bt2l`) ... |
f17f3074d9c2decf2f3e385a93c6b0f58a75a164c9d7a73f2fb92cc8b64ede7d | Rust | 25,814 | 653 | //! The Bismark alignment report (`<name>_bismark_bt2_SE_report.txt`) — a port of
//! the report header (Perl `start_methylation_call_procedure_single_ends`
//! 1642/1711–1729) and `print_final_analysis_report_single_end` (1964–2144),
//! plus the trailing wall-clock line (926–927).
//!
//! **Byte-identity gate** (Phas... |
e153cf0e55d00231659386b8cd04ee598b618276e7548ce5f611438f777883b1 | Rust | 26,823 | 745 | //! Input processing for cog predictors.
//!
//! This module handles file downloads for cog predictor inputs.
//! Input validation is performed at the HTTP edge using the OpenAPI schema;
//! the worker only needs to download URLPath inputs and pass them through.
use std::collections::HashSet;
use pyo3::prelude::*;
us... |
09354a39639c9c38bcb6059f4e1ab4d2063a402b833164c677e61d2ec7f4d861 | Rust | 26,854 | 582 | //! #1025 Phase 2 + Phase 3, Arc Institute BINSEQ (`.vbq` / `.cbq`) read input.
//!
//! Bismark has no native BINSEQ input. This module transcodes a BINSEQ file into a
//! temporary FASTQ that byte-matches what `bqtools decode` would emit, so the
//! **existing, byte-frozen** bisulfite-convert -> align -> merge pipelin... |
830735f15e68f2b9b7c8ccb616d414a4520b5796a8f66e3ceddff44636511840 | Rust | 26,982 | 738 | //! End-to-end integration tests for `methylation_consistency_rs`.
//!
//! Each test builds a synthetic Bismark BAM with the raw noodles writer (so we
//! can inject arbitrary records, including the XM-less record needed for the
//! graceful-stop test), runs the binary via `assert_cmd`, then reads the
//! output BAMs b... |
314f0f655078a6bd44b9c832a9583bdf6ce5ac647bfdb203f207319e7a2c0260 | Rust | 27,089 | 715 | //! #787 Illumina 5-Base DUPLEX-consensus pairing + per-molecule reconciliation.
//!
//! DRAGEN's 5-Base library is `nonrandom-duplex`: each original DNA molecule yields a
//! top-strand (OT) read and a bottom-strand (OB) read, tagged with complementary
//! ("swapped") UMIs. Pairing those two strands into a *duplex fam... |
5071b39bdbcf2f777dc5eba946562c3db9c90ba609b83fbf42ebd3d1269afd35 | Rust | 28,089 | 853 | //! Metric scope: type-safe metric recording with ContextVar routing.
//!
//! Two PyO3 classes:
//! - `Scope` — the per-prediction context, obtained via `current_scope()`
//! - `MetricRecorder` — the `scope.metrics` sub-object with type invariant
//! enforcement, dict-style access, and accumulation modes
//!
//! All ... |
36a2477b71f5116fde60b1fc004b2857e398dde66bcffd501203c1ed5f7e5432 | Rust | 30,474 | 773 | //! Bismark-flavoured CIGAR helpers as an extension trait on
//! [`noodles_sam::alignment::record_buf::Cigar`].
//!
//! Centralises the off-by-one-prone CIGAR arithmetic in one place so every
//! downstream binary inherits the same correct computation. In particular,
//! [`CigarExt::reference_end`] is the direct preven... |
6221f51b655e8390b99559ae5bdf9117cefac3e73140a6c17153e606da28debc | Rust | 34,058 | 802 | //! In-process rammap [`SamStream`] — the load-bearing seam for byte-identical
//! `bismark --rammap` WITHOUT spawning the `rammap` subprocess (epic
//! `06152026_rammap-library-integration`, Phase 1).
//!
//! For each converted FastQ read, [`InProcessAlignerStream`] calls
//! `rammap::Aligner::map_seq_with` and yields... |
23e993f63a2f91f924e70bf83d94156ab346930bcc2a9cb9cd87e43e4abc8939 | Rust | 34,072 | 825 | //! BAM, SAM, and CRAM writers consuming [`BismarkRecord`]s.
//!
//! Mirrors the structure of [`crate::io::read`]:
//!
//! - `BamWriter<W>`, `SamWriter<W>`, `CramWriter<W>` are the concrete
//! writers. Each has a `from_path` constructor and a generic `new`.
//! - `AnyWriter` enum + `open_writer` path-dispatcher cove... |
48aaf1482ef46d1aa67ad0a6c56bf2aea46384ec7143c01f2c0ccaa834a6882c | Rust | 34,246 | 824 | //! Bismark-aware record wrapper.
//!
//! [`BismarkRecord`] wraps [`noodles_sam::alignment::RecordBuf`] with eager
//! strand classification at parse time. The per-record strand is derived
//! once from the XR/XG tags and stored as a typed field — never recomputed.
//!
//! See `DESIGN.md` Q1 for the rationale: this is ... |
b92dd1c8c2d613c8acdf4821ef571b5badc25dd94a13d60e5d423d2bd75c891f | Rust | 34,746 | 868 | //! Phase 2 — in-process file-coupled orchestration of `bismark2bedGraph` +
//! `coverage2cytosine`.
//!
//! After extraction writes the per-context split files, the extractor drives
//! the bedGraph + cytosine-report tools **in-process** (no fork/exec, no Perl):
//! it builds the argv each standalone binary would rece... |
eed09dd61ca63d9345eac6c57b439e3d1e78cc13aee828301ae5e56a50414206 | Rust | 35,780 | 958 | //! Bridge between coglet-worker's PredictHandler trait and PythonPredictor.
use std::collections::HashMap;
use std::sync::{Arc, Mutex};
use std::thread::JoinHandle;
use pyo3::prelude::*;
use pyo3::types::PyDict;
use coglet_core::bridge::protocol::SlotId;
use coglet_core::worker::{PredictHandler, PredictResult, Setu... |
a8949e361b786bb6724c2f4a9a80910db9d99d1596e6d1ffb33c47d417846002 | Rust | 36,372 | 945 | use std::mem::{offset_of, size_of};
use crate::camera::Camera;
use crate::dim_check::DimCheck;
use crate::kernels::{
GatherGrads, GetTileBinEdges, MapGaussiansToIntersect, ProjectBackwards, ProjectSplats,
ProjectVisible, Rasterize, RasterizeBackwards,
};
use crate::BurnBack;
use brush_kernel::{
bitcast_te... |
8752faab1d026f2366921fb707309cf4af73a500b1f9f8c493844e9a679633bd | Rust | 37,551 | 888 | //! Assembly of the Bowtie 2 `aligner_options` string — **byte-identity-critical**.
//!
//! The push order below is verified against Perl `bismark` 7838–8142 and is the
//! literal option string each Bowtie 2 instance receives (the per-instance
//! `--norc`/`--nofw` is added later, NOT here). Order (rev-1, dual-review)... |
3c78b0c3aef4a9556aa2c2e18ade8a4c5f52404a210c5cfc34b6cb5c8580da43 | Rust | 37,745 | 1,060 | //! Worker subprocess - runs inside the Python subprocess.
//!
//! This module provides the child-side of the worker subprocess protocol.
//! The parent side (spawning, message routing) is in orchestrator.rs.
//!
//! Architecture:
//! - Control channel (stdin/stdout): Cancel, Shutdown signals + Ready, Idle responses
//... |
7c1fddaa63c1f2c91bbfee4fd404a964e4086e5e238e65681e796509ecd9dbbd | Rust | 38,922 | 1,016 | //! Phase 2 — in-process file-coupled orchestration: bridge-parity tests.
//!
//! These tests prove the **config bridge** between the extractor and the
//! in-process `bismark2bedGraph` / `coverage2cytosine` crates is correct:
//! the argv the extractor builds, the filenames it derives, and the kept-set
//! it forwards... |
b310744e382c653a431762fc709b551eba5949fd3ef1b4ae0bb8cd10c78bdf4d | Rust | 40,276 | 1,132 | //! Phase 9b — order-preserving file-level threading (`--multicore`/`--parallel`).
//!
//! `--parallel N` (N > 1) splits each read file (SE) or mate-pair (PE) into **N
//! contiguous chunks**, runs the full convert → 2–4 Bowtie 2 → lockstep-merge
//! pipeline ([`crate::aligner::process_se_chunk`]/[`crate::aligner::proc... |
5b1e38094055cf15c719f7a0d1ba633313bd22b04af23c598b945470b862e9d8 | Rust | 42,124 | 1,222 | //! Prediction state tracking.
use std::collections::{HashMap, VecDeque};
use std::sync::Arc;
use std::time::Instant;
use tokio::sync::Notify;
pub use tokio_util::sync::CancellationToken;
use crate::bridge::protocol::{LogSource, MetricMode};
use crate::webhook::{WebhookEventType, WebhookSender};
pub const STREAM_CH... |
cccf42570eeea16aeaf34e43cc6b8cac0d19fcd5d5ce76bcb36e6946557b39f6 | Rust | 42,663 | 1,137 | //! Command-line interface for `bismark_methylation_extractor`.
//!
//! All 35 Perl flags from [SPEC §3](../../SPEC.md) are mapped to clap-derived
//! fields below. [`Cli::validate`] returns a [`ResolvedConfig`] after
//! checking every documented mutex pair + precondition from SPEC §11 +
//! Perl source.
//!
//! ## Fl... |
d93c531aa7dbf07b1429bfd56080c2d8f868fffcdbd28ca327886e6cb87a7153 | Rust | 42,878 | 1,079 | //! #787 Illumina 5-Base SYNTHETIC GROUND-TRUTH gate, using the REAL minimap2.
//!
//! A true "concordance vs DRAGEN" gate is impossible without DRAGEN (proprietary
//! FPGA, no reference output) and without a public raw 5-Base dataset. This is the
//! achievable, stronger substitute: we synthesize reads from a known r... |
31d669f1887e05bf2993edbf34db0881cf71a1e1cf0c502451b65e5072223a26 | Rust | 44,654 | 1,158 | //! The core genome-wide cytosine report — the byte-identity crux.
//!
//! Mirrors Perl `generate_genome_wide_cytosine_report:168-745` +
//! `process_unprocessed_chromosomes:1388-1565`: stream the coverage file one
//! chromosome at a time, walk every `C`/`G` in that chromosome's genome
//! sequence with exact `pos = i... |
aa6e3695e69e74c6035c4e30fd27f73ad01b71f57d55a320bcdc5b55a06a1f1e | Rust | 46,589 | 1,205 | //! Phase B unit tests — kernel + routing + output map + state machinery.
//!
//! Organisation mirrors the plan §7.1 test list, grouped by module under
//! `#[cfg(test)] mod` blocks. Heavy synthetic-record construction sits in
//! a `helpers` module shared by all groups.
//!
//! End-to-end smoke that runs the binary on... |
434ff076a7b70915aac080f422d9ea727f06c3bdd3be69ab2365de496bd19cf4 | Rust | 46,771 | 1,294 | use chashmap::CHashMap;
use itertools::Itertools;
use programinduction::{
lambda::{self, Expression},
ECFrontier, Task,
};
use rayon::prelude::*;
use std::cmp::Ordering;
use std::collections::{HashMap, HashSet};
use std::f64;
use std::hash::{Hash, Hasher};
use std::sync::{Arc, Weak};
const EPSILON: f64 = 0.001... |
5c0fd654c0c3e14fe7687bb7dff5dbe5f3f3cf4c051f6a160de0dbdc274a83c5 | Rust | 48,756 | 1,218 | //! Genomic-sequence extraction + the `XM` methylation call — a port of Perl
//! `extract_corresponding_genomic_sequence_single_end` (4273–4467) and
//! `methylation_call` (4800–5018), plus `reverse_complement` (5161).
//!
//! For one `UniqueBest` alignment, pull the genomic window (read length + 2
//! context bases) m... |
62fa1bf9487bb813e784eab7e5a0f09e294d65d02736d46385373387ee524b41 | Rust | 55,093 | 1,454 | //! Phase F byte-identity tests.
//!
//! Three categories of assertion:
//! 1. **Legacy vs parallel** — `extract_se` / `extract_pe` (single-threaded,
//! Phase B/C reference) vs `extract_se_parallel` / `extract_pe_parallel`
//! (the new pipeline) on the same input. Byte-identical output is the
//! load... |
fc319fa3d1172f0e01c90a73dc37408406dfdaf8dd287f05a0517a922a80a710 | Rust | 56,238 | 1,443 | //! Dedup pipeline: orchestrates `bismark-io` reader/writer + the
//! [`crate::dedup::dedup::DedupState`] primitives into a working dedup loop.
//!
//! The two public entry points:
//!
//! - [`run_single`] — one input file, one output file, one report.
//! - [`run_multiple`] — N input files treated as one combined stre... |
b0a9072024bc9aadfb4625961c0bb6dd665057c550d2ce6ad395a95e901a1ced | Rust | 57,324 | 1,389 | //! BAM, SAM, and CRAM readers that yield [`BismarkRecord`]s.
//!
//! All three readers wrap their underlying noodles reader and produce
//! [`BismarkRecord`] via [`BismarkRecord::from_noodles_record`]. The
//! iterator-level adapter:
//!
//! - **Silently filters unmapped reads** (SAM FLAG & 0x4). The
//! [`BismarkRe... |
9c745baa5e9ec967414f3c4d6fd4a91e3a69427791c81aab3f205a782434e30b | Rust | 61,840 | 1,594 | //! Phase 3a — streaming bedGraph tee: byte-identity gate + ownership + D5.
//!
//! Phase 3a feeds methylation calls into a `bismark::bedgraph::Aggregator` IN
//! MEMORY during extraction (the tee at the shared `write_call` funnel) and
//! writes the `.bedGraph`/`.cov.gz` from `agg.into_sorted()` instead of
//! re-read... |
5beab878f787195ae1259c3efa477a45bc26188e5685b781e91f6eb549e79fc2 | Rust | 62,652 | 1,622 | //! Single-instance Bowtie 2 stream + SAM-line parse — the lockstep primitive.
//!
//! Spawns ONE Bowtie 2 subprocess against the converted temp FastQ, skips the
//! SAM header, and exposes a *peek + advance* interface (`current()` /
//! `advance()`) over parsed [`SamRecord`]s. Phase 4 drives 2–4 of these in
//! read-I... |
8abf77d150dda9619fd8947589964fe86f87bc5c513a790a9981ef3372cf2d27 | Rust | 63,761 | 1,780 | //! Bisulfite best-alignment merge — a port of Perl `check_results_single_end`
//! (2702–3151) for single-end directional reads (2 instances).
//!
//! For one original read, drive the per-instance [`SamStream`]s in read-ID
//! lockstep, pick the unique best alignment by `AS` across instances (handling
//! same-thread a... |
ffd4899f2fa5a694b48573f5ea5913fc6d564395a48c99b0d9c86445f0f7e4e0 | Rust | 64,059 | 1,401 | //! Per-(mode-key) split-file map + splitting-report writer.
//!
//! The `(key, filename)` list comes from [`crate::extractor::output_mode::mode_keys`]
//! (all 5 non-`MbiasOnly` modes); each file is a plain `File` or a parallel-gzip
//! `ParCompress<Gzip>` when `--gzip` is set. `MbiasOnly` yields an empty map
//! (`ro... |
80bf068835ef4974664d84fcc40f3d0764bdf9f93b3dec79cdbff26ae128c6be | Rust | 64,564 | 1,897 | //! PredictionService: Transport-agnostic prediction lifecycle management.
//!
//! This service is the single owner of prediction state. It manages:
//! - Slot management (PermitPool for concurrency control)
//! - Prediction lifecycle (DashMap of active predictions)
//! - Cancellation (cancel tokens + orchestrator dele... |
152eb6267d46e8c7fc06699d43316fd1d51d2ec7883771c886576105a2447a1a | Rust | 68,162 | 1,795 | //! Python predictor loading and invocation.
use std::sync::{Arc, OnceLock};
use pyo3::exceptions::PyValueError;
use pyo3::prelude::*;
use pyo3::types::{PyDict, PyTuple};
use coglet_core::worker::SlotSender;
use coglet_core::{PredictionError, PredictionOutput, PredictionResult};
use crate::cancel;
use crate::input:... |
0944af9aa879f36ee0bf5abce4be565bbed9b9a3da417d35d77c279d09333a4d | Rust | 68,839 | 1,656 | //! Phase C unit tests — PE extraction loop, overlap detection, per-mate
//! ignore trims, SE-vs-PE auto-detect.
//!
//! Test names mirror plan §7.1's labels. End-to-end smoke that runs the
//! binary on a synthetic PE BAM lives at `tests/pe_phase_c_smoke.rs`.
#![allow(non_snake_case)]
use bismark::extractor::call::{... |
f12cfe4c60a445f48db47fa1fbe3e8cf14756807c2128a2282c4fb99a5d58ce3 | Rust | 69,440 | 1,755 | //! Bisulfite read conversion — the C→T-converted temp FastQ that Bowtie 2 reads.
//!
//! Mirrors Perl `biTransformFastQFiles` (5489–5651) + `fix_IDs` (6235–6246) for
//! the v1 spine (FastQ, single-end, directional). The output temp file must be
//! **byte-identical** to Perl's so Bowtie 2 receives identical input. Th... |
92e896a9a990365db0c741f485d0deb3d19b1652961eecf93abd6eed4b028fcc | Rust | 71,058 | 1,624 | //! Phase F: rayon-based `--multicore N` pipeline (byte-identical to `--multicore 1`).
//!
//! Architecture per `SPEC.md §6.4 + §9` and `plans/05262026_bismark-extractor/PHASE_F_PLAN.md` rev 1:
//!
//! ```text
//! ┌─ worker 1 ─┐
//! input BAM ──▶ producer ──▶ worker 2 ──▶ collector ──▶ split files + M... |
d99b369786824aeacfce6f9c053fc80ec147aa9430bfa7f8d62aad1f62dd1b5a | Rust | 71,215 | 2,086 | //! HTTP route handlers.
use std::convert::Infallible;
use std::sync::Arc;
use std::time::Duration;
#[cfg(feature = "tracing")]
use axum::extract::MatchedPath;
use axum::{
Router,
body::Body,
extract::{DefaultBodyLimit, Path, State},
http::{HeaderMap, Request, StatusCode},
middleware::{self, Next}... |
ed2becab9b47c91e39fa27e1ec68681801f5c9d4d3418897fcf7ec9429e62c32 | Rust | 74,213 | 1,867 | //! SAM/BAM record + header assembly — a port of Perl `generate_SAM_header`
//! (8452–8484), `single_end_SAM_output` (8489–8711), `make_mismatch_string`
//! (9252–9595), `hemming_dist` (9235), and `revcomp` (9228).
//!
//! Builds the noodles [`Header`] (`@HD`/`@SQ`/`@PG`) and, per `UniqueBest`
//! alignment, a [`Bismar... |
6f72d94aa029c5135828181553bfed00105ed95d87bc3126181403e95a99615b | Rust | 75,494 | 1,851 | //! Orchestrator - manages worker subprocess lifecycle and event loop.
//!
//! Flow:
//! 1. Spawn worker subprocess
//! 2. Send Init message, wait for Ready
//! 3. Populate PermitPool with slot sockets
//! 4. Run event loop routing responses to predictions
//! 5. On worker crash: fail all predictions, shut down
use st... |
cd7d3c29b08d61222d1b5a685172afa4ba25e33e4b946ee9a33b15c57ea63abb | Rust | 85,576 | 2,323 | //! Integration tests for `deduplicate_bismark_rs` end-to-end.
//!
//! Each test:
//! 1. Constructs a synthetic Bismark BAM at a temp path via `bismark-io`'s
//! `BamWriter` (records hand-built with the right strand tags, CIGAR,
//! flags, etc.).
//! 2. Spawns the `deduplicate_bismark_rs` binary via `assert_cmd` ... |
f873f16a6957757287861cc699d1f78c8b0a322076a21fae904ebc3a6c3810c8 | Rust | 100,553 | 2,376 | //! `--combined_index` (v2) strand classification + per-read selection.
//!
//! **Opt-in, never-silent, concordance-gated — NOT byte-identical** to the
//! faithful per-strand-instance path. The combined index is searched in ONE
//! both-strands Bowtie 2 pass per read-conversion (`-k 2`, no `--norc`/`--nofw`);
//! each... |
3a0451194065dcdd43f4ebaddeb748754a1f90712eb668ce53d11185b27e3040 | Rust | 105,589 | 2,418 | //! Resolved run configuration — the typed seam (`RunConfig`) that Phase 1
//! produces and Phases 2–10 consume.
//!
//! [`resolve`] mirrors Perl `process_command_line`'s precedence: aligner →
//! library type → format → genome/reads → discovery → aligner detection →
//! `aligner_options` → output target. Only the **v1... |
75e991dac00d8414506bfa5d4f69bc04d431bb47701d8c2329f3eec7ecfe238e | Rust | 200,721 | 4,802 | //! `bismark-aligner` — Rust port of the Perl `bismark` aligner **wrapper**.
//!
//! `bismark` is not an aligner: it converts reads (C→T, plus the G→A complement
//! for non-directional), drives 2–4 external **Bowtie 2** instances against the
//! bisulfite-converted indexes, merges/scores their SAM in read-ID lockstep,... |
50539c93130b96099d1e081f0e351b38bd7414a0b35aad09c5d07c8795ac0a05 | Rust | 200,813 | 5,020 | //! End-to-end CLI tests for Phase 1 (`bismark_rs`): parse → discover → detect →
//! options → resolved-config summary, plus the deferral/validation error paths.
//!
//! Aligner detection runs `bowtie2 --version`; tests that reach detection use a
//! tiny **fake** `bowtie2` (reports `version 2.5.5`) via `--path_to_bowt... |
616ccd0d834669bd276115cd0158d47d6a5013577c1a1c4ff924118f157af2a2 | SAS | 2,016 | 76 | /* Generated Code (IMPORT) */
/* Source File: P americana experiment.jmp */
/* Source Path: /folders/myshortcuts/MyFolders */
/* Code generated on: 5/9/19, 5:04 PM; UPDATED 6/27/2024*/
/* Code for analyses of brown trout response to extra-large prey */
%web_drop_table(WORK.IMPORT1);
FILENAME REFFILE '/home/u1856827/M... |
ffcabebcfdbfc5664371f97898eca0b381fd41665a44a2a2e8147df5fb61b94e | SAS | 2,269 | 80 | /* Generated Code (IMPORT) */
/* Source File: Brown trout Prey Memory Analyses.jmp */
/* Source Path: /folders/myshortcuts/MyFolders */
/* Code generated on: 5/9/19, 12:57 PM; UPDATED 6/27/2024*/
/* Code for analysis of brown trout prey memory extinction */
%web_drop_table(WORK.memory);
FILENAME REFFILE '/home/u1856... |
4cc5303d3dc5664595c309f55089affd10daa1fe49a97aadc7fbe3b38ecad7b7 | SAS | 3,337 | 113 | /* Generated Code (IMPORT) */
/* Source File: ExposureRatioData.jmp */
/* Source Path: /home/u1856827/My SAS Files/Brown trout feeding */
/* Code generated on: 7/2/24, 4:19 PM */
%web_drop_table(WORK.IMPORT1);
FILENAME REFFILE '/home/u1856827/My SAS Files/Brown trout feeding/ExposureRatioData.jmp';
PROC IMPORT DATA... |
6a9c0b1e89944bb15bf2abf86cdd7ab91dae3aabf21d6d266614e763e3ec62d4 | SPSS | 457 | 8 | MIXED sc_AI BY Run Performance Instruction
/CRITERIA=DFMETHOD(SATTERTHWAITE) CIN(95) MXITER(100) MXSTEP(10) SCORING(1)
SINGULAR(0.000000000001) HCONVERGE(0, ABSOLUTE) LCONVERGE(0, ABSOLUTE) PCONVERGE(0.000001, ABSOLUTE)
/FIXED= Performance Run*Performance | SSTYPE(3)
/METHOD=ML
/PRINT=DESCRIPTIVES SOL... |
16450cd63475a668d862b8ce548ac1628f3e6ebf2d558873097898a51c7eda77 | SPSS | 459 | 8 | MIXED sc_dACC BY Run Performance Instruction
/CRITERIA=DFMETHOD(SATTERTHWAITE) CIN(95) MXITER(100) MXSTEP(10) SCORING(1)
SINGULAR(0.000000000001) HCONVERGE(0, ABSOLUTE) LCONVERGE(0, ABSOLUTE) PCONVERGE(0.000001, ABSOLUTE)
/FIXED= Performance Run*Performance | SSTYPE(3)
/METHOD=ML
/PRINT=DESCRIPTIVES S... |
ce97f0158fbd90aac61018c3e640a36a1a4216cf34c7d9ec2ee70c5d9628b250 | SPSS | 462 | 8 | MIXED sc_put BY Run Performance Instruction
/CRITERIA=DFMETHOD(SATTERTHWAITE) CIN(95) MXITER(100) MXSTEP(10) SCORING(1)
SINGULAR(0.000000000001) HCONVERGE(0, ABSOLUTE) LCONVERGE(0, ABSOLUTE) PCONVERGE(0.000001, ABSOLUTE)
/FIXED= Run Performance Run*Performance | SSTYPE(3)
/METHOD=ML
/PRINT=DESCRIPTIVES... |
a94fe69a1eb383116d1f19f63cbfbb52338653296e0dbcbe41c05651ea4bf7c6 | SPSS | 472 | 9 | MIXED Errors_number BY Run Instruction
/CRITERIA=DFMETHOD(SATTERTHWAITE) CIN(95) MXITER(100) MXSTEP(10) SCORING(1)
SINGULAR(0.000000000001) HCONVERGE(0, ABSOLUTE) LCONVERGE(0, ABSOLUTE) PCONVERGE(0.000001, ABSOLUTE)
/FIXED= Run Instruction | SSTYPE(3)
/METHOD=ML
/PRINT=DESCRIPTIVES SOLUTION
/RANDOM... |
f8e31d0a584f26a7e7b3d50fb855138cd3c075b4377a1307e4bcbade32136538 | SPSS | 1,708 | 63 | * Encoding: UTF-8.
* Attempt 1 on Making REDCap Data Export Cleanup *
*Open terminal, get the pathway for the bin folder of contents for SPSS statistics, then set cd to the bin folder there*
*cd /Applications/IBM\ SPSS\ Statistics/SPSS\ Statistics.app/Contents/bin *
*Need to install pandas: ./statisticspython3 -m p... |
9da586f0bacc9ffa6c86a4f84931874f28ab79eba544e507cd215abfdb1cfdd9 | Scala | 552 | 27 | import org.openbabel._
object OBTest {
def main(args: Array[String]) {
println("Loading openbabel_java...")
System.loadLibrary("openbabel_java")
println("Running OBTest...")
run
}
def run() {
val c = new OBConversion
val mol = new OBMol
c.SetInFormat("smi")
c.ReadString(mol, "... |
bc009bfbd072b2283ee639b39b096b1d1b4a8a3753807dd4ab86d567cd9b91fc | Shell | 15 | 1 | Rscript FigS1.R |
24b0081a84c613632dfc90b873c83543871bcf26df8dedf868b9b44652811109 | Shell | 17 | 1 | main/run_main.sh
|
f4d050b1914434fb849be8aacf28bde1d18fedb6c85cc5f2bd2e0357db57f5f1 | Shell | 31 | 1 | python setup.py build install
|
a598977a5604c9d15d1b77023a7adcd2646a426e31a5503159fefa182ff824ba | Shell | 35 | 3 | bbr_thr=0.6
max_FC=5
min_length=240 |
bd59c07c7286153efd94afa06e6513e65a3a0e8fa35221872f61854928c0d50e | Shell | 36 | 1 | python3 setup.py build_ext --inplace |
5a93e67ff69e61ad3263d15b8bccc733ade88d06dcb826e832ec94b8c366835c | Shell | 37 | 3 | for i in ../bin/test_*
do $i
done
|
727bb2d1619b26d6a6b8333d96322d3575f30d9480ac42e5a43f3441297c2017 | Shell | 39 | 2 | # run PlatformIO builds
platformio run
|
39cbaeb8bbbf3ffc531f81835b6039ef22b2d7e3ea1e4154ef557a570af950dc | Shell | 41 | 1 | docker run --rm -it ghcr.io/hdegen/hornet |
608c875b758a814914a0e10795ad7a94360bde3cf2c48c3f9dea4ef43412091f | Shell | 42 | 1 | # do nothing HIVE_HOME already set by env
|
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