sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
8150274ba2a704d4998d7d1353ae062af41b371e3b8d7fe353473dce4eeecfe2 | Rust | 1,303 | 41 | use crate::common::run_modkit;
mod common;
#[test]
fn test_entropy_help() {
run_modkit(&["entropy", "--help"]).expect("entropy help");
}
#[test]
fn test_entropy_regression() {
let td = std::env::temp_dir().join("test_entropy_regression");
std::fs::create_dir_all(&td).expect("should make temp dir");
r... |
e3c6481d656fd11c6763a192bdd27e6ce0ab7ba02cac4c9c8a4bdf4e92daf8b0 | Rust | 1,344 | 62 | extern crate core;
pub mod adjust;
pub mod bedmethyl_util;
// pub mod commands;
pub mod command_utils;
pub mod dmr;
pub mod entropy;
pub mod errs;
pub mod extract;
pub mod interval_chunks;
pub mod localise;
// pub mod logging;
pub mod mod_bam;
pub mod mod_base_code;
pub mod modbam_util;
pub mod monoid;
pub mod motifs;... |
5eb5f4aa9402ca3187ad48fbafe70a14d3feba70b722813b1551a768fc18e359 | Rust | 1,507 | 62 | use crate::common::{check_against_expected_text_file, run_modkit};
mod common;
#[test]
fn test_pileup_hemi_help() {
let pileup_help_args = ["pileup-hemi", "--help"];
let _out = run_modkit(&pileup_help_args).unwrap();
}
#[test]
fn test_pileup_hemi_hm() {
let temp_file = std::env::temp_dir().join("test_pil... |
de9e1194f07ba5a1294d0186a1774201c675e1ed0a0dbdde37f88615b1511602 | Rust | 1,556 | 53 | use nom::bytes::complete::tag;
use nom::character::complete::{
alphanumeric1, anychar, multispace1, none_of, u64 as nomu64,
};
use nom::multi::{fold_many1, separated_list0};
use nom::number::complete::float;
use nom::IResult;
pub(crate) fn consume_digit(l: &str) -> IResult<&str, u64> {
multispace1(l).and_then(... |
9617ed0302db891dcfbb81c344bf2d1ae412110d89d5683271eab0069114f6fc | Rust | 1,594 | 54 | use crate::common::run_modkit;
use anyhow::Context;
use std::fs::File;
use std::io::{BufRead, BufReader};
mod common;
#[test]
fn test_validate_help() {
run_modkit(&["validate", "--help"])
.context("validate --help failed")
.unwrap();
}
#[test]
fn test_validate_expected() {
let output_file = s... |
494333f82076af740a410b529f0d18ef91d23732f34db5c10b68a90fa404cc31 | Rust | 1,618 | 60 | use derive_new::new;
use serde::{Deserialize, Serialize};
use std::collections::HashMap;
use std::fmt::Debug;
use std::fs::File;
use std::path::Path;
use mod_kit::mod_base_code::{DnaBase, ModCodeRepr};
pub(crate) mod filenames {
pub const WEIGHTS_FN: &'static str = "model.mpk";
pub const CONFIG_FN: &'static s... |
5f0aacd7310af25e42a0ea4f2adda831bfc36fb978355b7479a9f141accf7bd2 | Rust | 2,161 | 80 | use rayon::prelude::*;
use rustc_hash::FxHashMap;
use crate::mod_base_code::ModCodeRepr;
use crate::monoid::Moniod;
use crate::motifs::{EnrichedMotif, KmerRef, RawBase};
#[inline]
pub(super) fn aggregate_base_counts_on_position(
kmer_counts: &[(KmerRef, u32)],
) -> FxHashMap<RawBase, FxHashMap<usize, u32>> {
... |
2284f192dcb2c6ca65fb3e41b3e93a5e2b801e7d792514050e4c42d23abd56fd | Rust | 2,245 | 80 | use crate::common::{
check_against_expected_text_file, check_legal_csv, run_modkit,
};
mod common;
#[test]
fn test_dmr_helps() {
let _ = run_modkit(&["dmr", "pair", "--help"])
.expect("failed to run modkit dmr pair help");
let _ = run_modkit(&["dmr", "multi", "--help"])
.expect("failed to ... |
7c967ac2a77b0a5eb18c5d93b7303d4f1938095398edfd362c2820882fb1e792 | Rust | 2,342 | 79 | use crate::common::{check_against_expected_text_file, run_modkit};
use mod_kit::util::GenomeRegion;
use std::fs::File;
use std::io::{BufRead, BufReader};
use std::path::{Path, PathBuf};
mod common;
#[test]
fn test_open_chromatin_help() {
run_modkit(&["open-chromatin", "--help"]).expect("should run help");
run... |
49cc802ac8cd7a26a7345ee1e0e483e0f7a442ab234eb9d93f488107a7f8b2ae | Rust | 2,526 | 89 | use std::collections::HashMap;
use mod_kit::mod_bam::MN_TAG;
use rust_htslib::bam;
use rust_htslib::bam::Read;
use crate::common::{run_modkit, run_simple_summary};
mod common;
#[test]
fn test_repair_help() {
run_modkit(&["repair", "--help"]).unwrap();
}
#[test]
fn test_repair_regression() {
let out_bam = s... |
b8923ddfea3db3ed28fc5158405a51a95fd70653798dcd470c3ca178ad3c8bd9 | Rust | 2,537 | 93 | use std::fs::File;
use std::io::{self, BufRead, BufReader, Read};
use std::path::Path;
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
enum InputKind {
Plain,
Bgzip,
GzipButNotBgzip,
}
/// Detect whether a file is BGZF/bgzip-compressed.
///
/// BGZF is gzip with:
/// - gzip magic bytes: 1f 8b
/// - compressi... |
55630ac4e62fd98543f4e885e7ba3353af8b94e5ee49323604bc1f798ffab749 | Rust | 2,918 | 107 | use crate::util::{get_master_progress_bar, get_ticker};
use indicatif::ProgressBar;
use rand::rngs::StdRng;
use rand::{Rng, SeedableRng};
/// A utility data structure that when used in an interator allows
/// to randomly sample either a preset number of reads or a fraction
/// of reads. If sampling a preset number o... |
e3092d48db275bf894005e6b7967a00160cb841156e19709ab311dc44ad5c1ec | Rust | 3,135 | 101 | use derive_new::new;
use prettytable::{cell, row};
use rayon::prelude::*;
use rustc_hash::{FxHashMap, FxHashSet};
use crate::dmr::bedmethyl::BedMethylLine;
use crate::mod_base_code::ModCodeRepr;
use crate::monoid::Moniod;
use crate::tabix::HtsTabixHandler;
use crate::util::{GenomeRegion, ModPositionInfo, StrandRule};
... |
f5d6526e7e9fc7228b159261fe032dabe4c6e0fc58e24d782ea86d1763132cf9 | Rust | 3,349 | 115 | use std::string::FromUtf8Error;
pub type MkResult<T, E = MkError> = Result<T, E>;
#[derive(thiserror::Error, Debug)]
pub enum MkError {
// Tag parsing
#[error("invalid-aux-tags")]
InvalidTags,
#[error("invalid-MM-tag")]
InvalidMm(String),
#[error("invalid-ML-tag")]
InvalidMl(String),
#... |
a8fc40f7eda5e772336a0d740262348e30fca4c1f6988592945f7b80bfb0be58 | Rust | 3,656 | 122 | use rust_htslib::bam::{self, HeaderView};
use rust_htslib::htslib::bam1_t;
use std::rc::Rc;
pub struct SafeRecord {
inner: bam1_t,
}
unsafe impl Send for SafeRecord {}
unsafe impl Sync for SafeRecord {}
impl SafeRecord {
pub fn ingest(read: &mut bam::Record) -> Self {
let dummy = bam::Record::new();
... |
2954eb0094418d1752c61796bce6d360ef11b5bff01ee96e5e39bbdc7ec4c749 | Rust | 3,755 | 111 | use std::fs::File;
use std::path::PathBuf;
use anyhow::Context;
use log::{debug, LevelFilter};
use log4rs::append::console::{ConsoleAppender, Target};
use log4rs::append::file::FileAppender;
use log4rs::config::{Appender, Root};
use log4rs::encode::pattern::PatternEncoder;
use log4rs::filter::threshold::ThresholdFilte... |
874016e3b96ed5199e7f2eb95006c11c103acbfddb3d77d65ff265233d450782 | Rust | 4,333 | 132 | pub(crate) mod conv_lstm {
use burn::config::Config;
use burn::module::Module;
use burn::nn::conv::{Conv2d, Conv2dConfig};
use burn::nn::{
BatchNorm, BatchNormConfig, Linear, LinearConfig, Lstm, LstmConfig,
Relu,
};
use burn::prelude::Backend;
use burn::tensor::Tensor;
#... |
8791c0f0ad1044515b5a746ba6fb5721c8caf12e4d86dc878219b12ac0ee230f | Rust | 4,565 | 132 | use std::collections::HashSet;
use std::fmt::Debug;
use std::hash::Hash;
use std::ops::Range;
use std::path::PathBuf;
use indicatif::{MultiProgress, ProgressIterator};
use log::debug;
use rustc_hash::{FxHashMap, FxHashSet};
use crate::fasta::HtsLibFastaRecords;
use crate::mod_base_code::DnaBase;
use crate::util::{get... |
a22396ec743b03746eaacab9f1b987ad8159105d71aa57b2c83db9ba1ac1c820 | Rust | 4,962 | 181 | use statrs::distribution::{ChiSquared, ContinuousCDF};
use statrs::function::gamma::ln_gamma;
// #[derive(Debug, Clone)]
// pub(super) struct IsoformMethylationCounts {
// /// Counts for categories such as:
// /// [methylated_a, methylated_b, unmethylated]
// pub counts: Vec<u64>,
// }
#[derive(Debug, Clo... |
aed17fc10a782cdb89701991c1dcd8e330bd265fc2823ffe664b5e26b376b46a | Rust | 5,445 | 132 | use std::path::PathBuf;
use anyhow::{anyhow, bail, Context};
use log::{debug, error};
use rayon::prelude::*;
use rust_htslib::bam;
use mod_kit::mod_base_code::{DnaBase, ModCodeRepr};
use mod_kit::threshold_mod_caller::MultipleThresholdModCaller;
use mod_kit::util::Region;
use crate::features;
use crate::features::Co... |
df7910af836c4bfe5d30be56207a9832885313f31466a27700f656cf766714a1 | Rust | 5,477 | 171 | use crate::common::{
run_modkit, run_simple_summary, run_simple_summary_with_collapse_method,
run_simple_summary_with_edge_filter, run_summary_with_include_positions,
};
use anyhow::Context;
use mod_kit::mod_bam::{CollapseMethod, EdgeFilter};
use mod_kit::mod_base_code::{BaseState, DnaBase};
use std::collection... |
74fcc8fe5ce4a3863b71a26948551af9ea310a9c706f7023adf1cb774c77d9c3 | Rust | 6,149 | 204 | use bitvec::order::Lsb0;
use bitvec::vec::BitVec;
use derive_new::new;
use log::debug;
use rust_htslib::bam;
use crate::dmr::bedmethyl::BedMethylLine;
use crate::mod_bam::CollapseMethod;
use crate::mod_base_code::{DnaBase, ModCodeRepr};
use crate::util::StrandRule;
pub(crate) mod base_mods_adapter;
pub(crate) mod bed... |
8129a91bc4ac7502c62591f25d01a6fec160b14530ef2155484fb624aa9df3f2 | Rust | 6,225 | 198 | use std::{
fs::File,
io::{BufRead, BufReader, BufWriter, Read, Write},
};
use common::run_modkit;
use mod_kit::dmr::bedmethyl::BedMethylLine;
mod common;
#[test]
fn test_merge_bedmethyl_help() {
run_modkit(&["bedmethyl", "--help"]).unwrap();
run_modkit(&["bedmethyl", "merge", "--help"]).unwrap();
... |
44c64b69d3441628ca858824f5b350b3e4a5cb486103ca6cfa8c10b228fb6988 | Rust | 6,326 | 210 | use std::marker::PhantomData;
use std::ops::Range;
use std::path::PathBuf;
use anyhow::Context;
use itertools::Itertools;
use log_once::debug_once;
use rust_htslib::tbx::{Read, Reader as TbxReader};
use rustc_hash::FxHashMap;
use crate::dmr::bedmethyl::BedMethylLine;
use crate::errs::{MkError, MkResult};
use crate::m... |
9627d40b7daddc42588008d6aa37e2ff9b100fab85e1b8978ecdfecc1315da36 | Rust | 6,425 | 148 | use anyhow::Result as AnyhowResult;
use clap::Subcommand;
use mod_kit::bedmethyl_util::subcommands::EntryBedMethyl;
use mod_kit::dmr::subcommands::BedMethylDmr;
use mod_kit::entropy::subcommand::MethylationEntropy;
use mod_kit::extract::subcommand::ExtractMods;
use mod_kit::localise::subcommand::EntryLocalize;
use mod_... |
c3870f35ccb9272f17fbe67dd4c84cb351c88e1fde6445e07b89a1af58b3db4e | Rust | 6,529 | 192 | use crate::features::CountsFeatures;
use derive_new::new;
use log::debug;
use mod_kit::util::TAB;
use ndarray::{s, Array1};
use rustc_hash::FxHashMap;
use std::collections::{BTreeMap, VecDeque};
use std::fmt::{Display, Formatter};
use std::ops::Div;
#[derive(new, Debug)]
pub(crate) struct OpenChromRecord {
pub(cra... |
ed58961d7434be2e18624e7f40196e946a01b2e1c962381b7ea3c94f95e42eee | Rust | 6,981 | 245 | use anyhow::{anyhow, bail, Result as AnyhowResult};
use derive_new::new;
use mod_kit::mod_bam::{CollapseMethod, EdgeFilter};
use mod_kit::position_filter::StrandedPositionFilter;
use mod_kit::summarize::{summarize_modbam, ModSummary};
use mod_kit::threshold_mod_caller::MultipleThresholdModCaller;
use serde::Deserialize... |
a3031da9134a88d448feb88214097ad863196809c96eef29e346582e3f5e5e99 | Rust | 7,026 | 246 | use anyhow::{anyhow, bail, Result as AnyhowResult};
use derive_new::new;
use mod_kit::mod_bam::{CollapseMethod, EdgeFilter};
use mod_kit::position_filter::StrandedPositionFilter;
use mod_kit::summarize::{summarize_modbam, ModSummary};
use mod_kit::threshold_mod_caller::MultipleThresholdModCaller;
use serde::Deserialize... |
efe0fbafbad412b3a73182885f18c9556e545c4222ceec7843d392e9b0735d37 | Rust | 7,057 | 221 | use std::io::BufRead;
use bigtools::{
bed::bedparser::{BedValueError, StreamingBedValues},
Value,
};
use indicatif::ProgressBar;
use log::debug;
use rustc_hash::FxHashSet;
use crate::{
dmr::bedmethyl::BedMethylLine,
errs::{MkError, MkResult},
mod_base_code::ModCodeRepr,
util::StrandRule,
};
p... |
62cc7c2129fbcc27b38907291438917a2239c6e8a88cd37ea0d7617ced47b963 | Rust | 7,104 | 265 | use std::collections::HashMap;
use derive_new::new;
use std::fmt::Write;
use crate::dmr::{
bedmethyl::BedMethylLine,
isoform::{Exon, GeneModel, GtfTranscript},
};
#[derive(new)]
pub(super) struct GenomeSortedTranscriptModel {
pub strand: char, // '+' or '-'
pub exons: Vec<Exon>, // ordered in tra... |
146593acc6c5784c93d153f11ec2e9d082e7a42879b8b825b964a6a9d3c3df8f | Rust | 7,563 | 172 | use clap::{arg, Args};
use std::path::PathBuf;
#[derive(Args, Clone, Debug)]
pub(super) struct InputArgs {
/// Input bedmethyl table, can be used directly from modkit pileup.
#[clap(help_heading = "Input Options")]
#[arg(short = 'i', long)]
pub in_bedmethyl: PathBuf,
/// Number of threads to use.
... |
cdc8cf39c6b7192011314f620f1eb646d73785366136089736d2fbd8ab470ba3 | Rust | 7,728 | 260 | use std::collections::HashMap;
use std::path::PathBuf;
use crate::errs::{MkError, MkResult};
use crate::mod_bam::{CollapseMethod, EdgeFilter};
use crate::mod_base_code::{DnaBase, ModCodeRepr};
use crate::position_filter::StrandedPositionFilter;
use crate::read_ids_to_base_mod_probs::ReadIdsToBaseModProbs;
use crate::r... |
142a10d7a4d6a947319ae3b90602d950ddb81c28afa4b03b2647bf3a152f78d1 | Rust | 7,741 | 235 | use anyhow::{anyhow, bail};
use charming::component::{
Axis, DataZoom, DataZoomType, Feature, Legend, Restore, SaveAsImage, Title,
Toolbox, ToolboxDataZoom,
};
use charming::datatype::{CompositeValue, DataPoint, NumericValue};
use charming::element::{AxisType, LineStyle, Orient, Symbol};
use charming::series::L... |
c9282e37285522b273b566c2cc2e008422c60061eacffa04a09be8ab31ac14dc | Rust | 7,942 | 243 | use mod_kit::util::{GenomeRegion, Region};
use rust_htslib::bam::{self, Read};
use std::collections::{HashMap, VecDeque};
use std::fs::File;
use std::io::{BufRead, BufReader};
use std::ops::Range;
use std::path::PathBuf;
use crate::util::InferenceMessage;
use anyhow::{anyhow, bail, Context};
use itertools::Itertools;
... |
53e61bcb61adf548d3c98365df41d7358698356d3e538a0cd0e66a763d536254 | Rust | 7,973 | 218 | use std::fs::File;
use std::io::{stdout, BufRead, BufReader, BufWriter, Write};
use std::path::PathBuf;
use anyhow::{anyhow, bail};
use clap::Args;
use indicatif::{ParallelProgressIterator, ProgressIterator};
use itertools::Itertools;
use log::{debug, error, info};
use log_once::info_once;
use rayon::prelude::*;
use r... |
96bacfd26dae5dcae40f0b64ba13769fc0c28275ba379d72b29805cc92d95ba4 | Rust | 8,176 | 374 | use rustc_hash::{FxHashMap, FxHashSet};
use std::collections::{BTreeMap, HashMap, HashSet};
use std::hash::Hash;
pub trait Moniod {
fn zero() -> Self;
fn op(self, other: Self) -> Self;
fn op_mut(&mut self, other: Self);
fn len(&self) -> usize;
}
pub trait BorrowingMoniod {
fn zero() -> Self;
f... |
910e25cc2f19c2444a99fe0c55a2520b77976ad94ab9baefe1f3aacc8b68e603 | Rust | 8,592 | 181 | use clap::Args;
use std::path::PathBuf;
#[derive(Args)]
pub(super) struct InputArgs {
/// Path to modBAM file to extract read-level information from, or one of
/// `-` or `stdin` to specify a stream from standard input. If a file
/// is used it may be sorted and have associated index.
pub in_bam: Strin... |
75b6557db990b1ef21a695d1b199da994ea11d39ab5856b279225bf97a050e18 | Rust | 9,655 | 240 | use anyhow::anyhow;
use clap::Args;
use itertools::Itertools;
use linear_map::LinearMap;
use log::warn;
use rust_htslib::bam;
use rustc_hash::FxHashMap;
use crate::mod_base_code::{
DnaBase, ModCodeRepr, ModifiedBasesOptions, RNA_CODES_TO_MODOMICS_NAMES,
};
use crate::writers::bedrmod_bedmethyl_header;
#[derive(Ar... |
044d3982ef12bc03a3b4e4dca1a71d8d4589085cca774867db0f1494b47a085f | Rust | 10,527 | 332 | use crate::dmr::llr_model::AggregatedCounts;
use anyhow::{anyhow, bail};
use log::info;
use rv::dist::Beta;
use rv::misc::gauss_legendre_quadrature;
use statrs::function::beta::ln_beta;
use std::fmt::{Display, Formatter};
const LOWER: f64 = 1e-5;
const UPPER: f64 = 1f64 - LOWER;
fn appell_f1_stable(x: f64, y: f64, a:... |
77637c05d34662bda2bdfeedf7cb43b9c88f370acf1eff7068d470471ab2903e | Rust | 10,994 | 344 | use std::cmp::Ordering;
use std::collections::HashMap;
use std::path::Path;
use anyhow::bail;
use derive_new::new;
use rust_htslib::bam::{self, FetchDefinition, Read};
use rustc_hash::FxHashMap;
use crate::interval_chunks::{FocusPositions2, MultiChromCoordinates};
use crate::mod_bam::{DuplexModCall, DuplexPattern, Ed... |
5507920006590a352567b064a08726c9b437cc4f3b0bd335214f807027f4b536 | Rust | 11,071 | 326 | use crate::common::run_modkit;
use anyhow::{anyhow, Context};
use mod_kit::dmr::bedmethyl::BedMethylLine;
use mod_kit::errs::MkError;
use mod_kit::mod_bam::{
BaseModCall, ModBaseInfo, RawModTags, SeqPosBaseModProbs,
};
use mod_kit::mod_base_code::{
DnaBase, ModCodeRepr, ParseChar, METHYL_CYTOSINE, SIX_METHYL_AD... |
837e7cd0ae9044b20a4aaf70bd41287dc2a48e70449d20ada1445b15a1428133 | Rust | 11,512 | 310 | use std::collections::HashMap;
use std::fs::File;
use std::io::{stdout, BufRead, BufReader, BufWriter, Write};
use std::path::PathBuf;
use std::sync::Arc;
use anyhow::{anyhow, bail};
use clap::Args;
use indicatif::{MultiProgress, ParallelProgressIterator, ProgressIterator};
use itertools::Itertools;
use log::{debug, i... |
2a43d6dc4c0305d9be691e440a12b97bb78774ae9e589ef20be3abda7e56d7b6 | Rust | 11,527 | 358 | use derive_new::new;
use itertools::Itertools;
use log::debug;
use regex::Regex;
use rustc_hash::{FxHashMap, FxHashSet};
use std::collections::{BTreeSet, HashMap};
use std::str::Chars;
use substring::Substring;
#[derive(new)]
struct AlphabetInfo {
columns: FxHashMap<usize, String>,
}
impl AlphabetInfo {
fn fr... |
3b899aa0d44febf06c0f58620434b82e17ab8490183cd8fcc46115e7b991816b | Rust | 11,870 | 310 | use std::sync::Arc;
use crate::dmr::bedmethyl::{aggregate_counts, BedMethylLine};
use crate::dmr::llr_model::{AggregatedCounts, ModificationCounts};
use crate::dmr::tabix::{ChromToSampleBMLines, MultiSampleIndex};
use crate::dmr::util::{DmrBatch, RegionOfInterest, RoiIter};
use crate::errs::{MkError, MkResult};
use cr... |
102700b5030bd0602a7994eb858ca947b6c5fb48298bd0f2447f397bec1607a5 | Rust | 12,099 | 349 | use crate::entropy::{EntropyCalculation, WindowEntropy};
use crate::errs::MkError;
use crate::util::{Strand, TAB};
use anyhow::{anyhow, bail};
use indicatif::ProgressBar;
use log::debug;
use rustc_hash::FxHashMap;
use std::collections::HashMap;
use std::fs::File;
use std::io::{stdout, BufWriter, Write};
use std::ops::A... |
34f10b7c38794721ec5fcb7e4b02ad63d631c58a2d5a15ae7d340c8c42b8d392 | Rust | 12,215 | 358 | use std::{collections::HashSet, path::Path};
use anyhow::bail;
use bitvec::bitvec;
use indexmap::IndexMap;
use indicatif::MultiProgress;
use itertools::Itertools;
use log::debug;
use rustc_hash::FxHashMap;
use crate::{
dmr::{
bedmethyl::BedMethylLine,
isoform::{
dirichlet_multinomial_l... |
f8b17f9da2ab45dbbc6a3268cd0712afc61747686146c9962a18c0e5e538b12e | Rust | 12,449 | 368 | use std::path::PathBuf;
use anyhow::{bail, Context};
use bitvec::bitvec;
use bitvec::vec::BitVec;
use itertools::Itertools;
use log::debug;
use rayon::prelude::*;
use rust_htslib::faidx;
use rustc_hash::FxHashMap;
use substring::Substring;
use crate::errs::{MkError, MkResult};
use crate::interval_chunks::FocusPositio... |
ec3b9a97eb348603c19290c937db91bae959c56058b5a87810cf54ede0be4081 | Rust | 12,557 | 424 | use std::fmt::{Display, Formatter};
use std::ops::Range;
use anyhow::bail;
use log_once::debug_once;
const STATE_NUM: usize = 2usize;
#[derive(Copy, Clone, Debug, Eq, PartialEq, Hash, Ord, PartialOrd)]
#[repr(usize)]
pub(crate) enum States {
Same = 0,
Different = 1,
}
impl Into<usize> for States {
fn in... |
4137f15375a1644590fd68c58754414bf2c6d7721c659ca78c0e1a1d8e5cc4f2 | Rust | 12,681 | 391 | use std::path::PathBuf;
use anyhow::anyhow;
use indicatif::{MultiProgress, ProgressBar};
use itertools::Itertools;
use log::debug;
use prettytable::row;
use rayon::prelude::*;
use rust_htslib::bam::{self, Read};
use rustc_hash::FxHashMap;
use crate::interval_chunks::{
ChromCoordinates, ReferenceIntervalBatchesFee... |
e643d1c3e5de138029b50e0228908294fcaacc19b799f3ccda9acf736e93f6c7 | Rust | 12,804 | 374 | use std::collections::{HashMap, HashSet, VecDeque};
use std::fs::File;
use std::io::{BufRead, BufReader};
use std::path::PathBuf;
use anyhow::bail;
use itertools::Itertools;
use log::{debug, info};
use log_once::info_once;
use rust_htslib::bam::{self, Read};
use rust_lapper as lapper;
use rustc_hash::FxHashMap;
use c... |
842b2967e0c12e46037e8c26b19eec4afcf33784c8b07d25d4fef38b675c481e | Rust | 13,674 | 437 | use std::collections::{HashMap, HashSet};
use std::fmt::{Display, Formatter};
use anyhow::{anyhow, bail};
use itertools::Itertools;
use log::debug;
use rv::prelude::*;
use crate::dmr::util::{cohen_h, CohenHResult, DmrInterval};
use crate::errs::{MkError, MkResult};
use crate::mod_base_code::ModCodeRepr;
use crate::mo... |
70e9cdc042f795dccb42ab4ccdeda610e07d96d522347dfcd5cf04e582073eb5 | Rust | 13,697 | 374 | use std::collections::{BTreeMap, HashSet};
use std::fmt::Debug;
use std::ops::Range;
use anyhow::bail;
use rayon::prelude::*;
use rustc_hash::{FxHashMap, FxHashSet};
use crate::dmr::bedmethyl::{aggregate_counts2, BedMethylLine};
use crate::dmr::llr_model::AggregatedCounts;
use crate::dmr::util::{n_choose_2, DmrBatch,... |
92687825cae109b4ecf63d911133aec237502da24d4c7f0c6d511d5042983f6e | Rust | 13,732 | 394 | use std::path::PathBuf;
use std::sync::Arc;
use anyhow::{anyhow, bail, Context};
use clap::Args;
use derive_new::new;
use indicatif::{MultiProgress, ProgressBar};
use log::{debug, error, info, warn};
use rayon::prelude::*;
use rust_htslib::bam::record::{Aux, AuxArray};
use rust_htslib::bam::{self, Read};
use rustc_has... |
38eaccb0dbca1d7587b2a9c654dde8d4ee24a0c952aa67a75f8bdbe7ff1a0eb9 | Rust | 14,085 | 459 | use std::cmp::Ordering;
use std::collections::{BTreeMap, HashMap};
use std::fmt::{Display, Formatter};
use std::str::FromStr;
use crate::errs::{MkError, MkResult};
use crate::motifs::iupac::nt_bytes;
use anyhow::{anyhow, bail};
use clap::ValueEnum;
use common_macros::hash_map;
use derive_new::new;
use lazy_static::laz... |
a048324c08f9a9ff4cefca527aa41c3fa3f8f65fb988b5193caf2522af512935 | Rust | 14,299 | 438 | use anyhow::bail;
use derive_new::new;
use log::{debug, error, info};
use rayon::prelude::*;
use rust_htslib::bam::record::{Aux, AuxArray};
use rust_htslib::bam::{self, Read};
use rustc_hash::{FxHashMap, FxHashSet};
use std::ops::AddAssign;
use crate::errs::{MkError, MkResult};
use crate::mod_bam::{
format_mm_ml_t... |
3ef38fefb5b364a95f4fcc6b79e43aeb40251ca072d07f95fc05658cbb12ec3b | Rust | 14,638 | 483 | use crate::common::{parse_mod_profile, run_simple_summary};
use anyhow::Context;
use common::{check_legal_csv, run_modkit};
use mod_kit::mod_bam::RawModTags;
use mod_kit::mod_base_code::{BaseState, DnaBase};
use rust_htslib::{bam, bam::Read};
use std::path::PathBuf;
mod common;
#[test]
fn test_help() {
let pileup... |
95939f8d2a2dd62a4bcb20afd55914f4d3f8a594ac8aa462da97794505dd115c | Rust | 14,828 | 452 | use std::collections::HashMap;
use std::fs::File;
use std::io::{BufWriter, Cursor, Write};
use std::path::Path;
use indicatif::MultiProgress;
use crate::extract::util::ReadModsStatsRecord;
use crate::mod_bam::BaseModCall;
use crate::motifs::motif_bed::MotifPositionLookup;
use crate::read_ids_to_base_mod_probs::{
... |
bbf7d1576f769040c2cdfc78709f0251600d1afff75649122245d532a451d32d | Rust | 14,958 | 456 | use std::collections::HashMap;
use std::path::PathBuf;
use anyhow::{anyhow, bail, Context};
use itertools::Itertools;
use log::{debug, info, warn};
use rust_htslib::bam::{self, Header};
use crate::adjust::OverlappingRegexOffset;
use crate::fasta::MotifLocationsLookup;
use crate::mod_bam::{prob_to_qual, CollapseMethod... |
6868192348b8417800c9083720d39c1be966747048ec99a585b11359d8ae5628 | Rust | 15,483 | 466 | use crate::errs::MkError;
use crate::mod_bam::{
CollapseMethod, EdgeFilter, MmTagInfo, ModBaseInfo, RawModTags, SkipMode,
ML_TAGS, MM_TAGS,
};
use crate::mod_base_code::{DnaBase, ModCodeRepr};
use crate::monoid::Moniod;
use crate::position_filter::StrandedPositionFilter;
use crate::reads_sampler::record_sampler... |
923445b42d518bc7f9529d6ccc2fce25856405f1b859e2713755a67c404a5ec3 | Rust | 15,997 | 453 | use std::collections::{HashMap, HashSet};
use std::fmt::Display;
use anyhow::Context;
use derive_new::new;
use itertools::{Itertools, MinMaxResult};
use log_once::debug_once;
use nom::character::complete::{multispace1, none_of};
use nom::combinator::map_res;
use nom::multi::many1;
use nom::IResult;
use rustc_hash::{Fx... |
1ec81c1712381683388ed9fe04ad4ef7973ecf2a4d112f17b6c4b1c3e6840d6e | Rust | 16,797 | 429 | use std::cmp::Ordering;
use std::io::{BufWriter, Write};
use std::path::PathBuf;
use anyhow::{bail, Context};
use burn::data::dataloader::batcher::Batcher;
use burn::module::Module;
use burn::prelude::Backend;
use burn::record::{CompactRecorder, Recorder};
use burn::tensor::activation::softmax;
use clap::{Args, Subcom... |
1e25a3660aef58adaa372163117471978ae02253da91b48df136bec9b2ce2a3b | Rust | 17,624 | 614 | use crate::common::{
check_against_expected_text_file, parse_mod_profile, ModData,
};
use anyhow::{anyhow, Context};
use common::{check_legal_csv, run_modkit, ExtractFullRecord};
use std::collections::{HashMap, HashSet};
use std::fs::File;
use std::io::BufRead;
use std::io::BufReader;
use std::path::{Path, PathBuf}... |
1365cb7348ded81abc658e11d6270a95eb8f537f7ece1c0f28389765830d4163 | Rust | 18,873 | 488 | use std::collections::{HashMap, HashSet};
use std::path::PathBuf;
use common_macros::hash_map;
use derive_new::new;
use indicatif::{MultiProgress, ParallelProgressIterator};
use log::{debug, error, info};
use rayon::prelude::*;
use crate::mod_bam::{prob_to_qual, BaseModCall, CollapseMethod, EdgeFilter};
use crate::m... |
9bed36b3a72c42fb519d17521b3833d3da8f66cd5622da67c630e82d1eeb90b7 | Rust | 19,248 | 482 | use crate::mod_bam::{BaseModCall, BaseModProbs, SeqPosBaseModProbs, SkipMode};
use crate::mod_base_code::{DnaBase, ModCodeRepr};
use derive_new::new;
use rustc_hash::FxHashMap;
use std::collections::HashMap;
#[derive(new, Clone)]
pub struct MultipleThresholdModCaller {
per_base_thresholds: HashMap<DnaBase, f32>,
... |
e76e517a78a42da2ffbb5387cf3518196e1e09711c54a264b257d59f00aee9f8 | Rust | 20,123 | 646 | use std::cmp::Ordering;
use std::collections::VecDeque;
use std::fmt::{Debug, Display, Formatter};
use std::fs::File;
use std::io::{BufRead, BufReader};
use std::path::Path;
use std::sync::Arc;
use crate::dmr::llr_model::AggregatedCounts;
use crate::dmr::tabix::MultiSampleIndex;
use crate::genome_positions::{GenomePos... |
8bddee4bd2fbaf34060afef43b055281d511c06443ace1016c04605672803a9a | Rust | 20,190 | 539 | use std::collections::HashSet;
use log::{debug, error};
use log_once::info_once;
use rust_htslib::bam;
use rustc_hash::{FxHashMap, FxHashSet};
use crate::errs::{MkError, MkResult};
use crate::mod_bam::{
BaseModCall, CollapseMethod, DuplexModCall, EdgeFilter, ModBaseInfo,
SeqPosBaseModProbs, SkipMode,
};
use c... |
a9ff613293034fac34971a9294ad1f0e80ccc95cf7d98f15680d6729c9cd27e4 | Rust | 20,975 | 518 | use std::collections::HashMap;
use std::path::PathBuf;
use std::sync::Arc;
use anyhow::{bail, Context};
use clap::Args;
use indicatif::MultiProgress;
use log::{debug, error, info};
use rayon::prelude::*;
use rustc_hash::FxHashMap;
use modkit_logging::init_logging;
use crate::command_utils::parse_per_mod_thresholds;
... |
48a41ddc8722f807d25391b596a90b0cd4e7f3591b4d177b0dacf9935e8dcf22 | Rust | 22,120 | 681 | use std::collections::{BTreeMap, BTreeSet, HashMap};
use std::ops::ControlFlow;
use anyhow::{anyhow, bail, Context};
use derive_new::new;
use itertools::Itertools;
use ndarray::{Array2, Axis};
use rayon::prelude::*;
use rust_htslib::bam::pileup::Indel;
use rust_htslib::bam::{self, FetchDefinition, Read};
use rustc_has... |
836ca61678ee3f3b582251d13477decd5e6c131000a9a8c79f7ecb5fe15f59dc | Rust | 23,413 | 700 | use std::collections::{BTreeMap, BTreeSet, VecDeque};
use anyhow::{anyhow, bail};
use bitvec::bitvec;
use bitvec::order::Lsb0;
use bitvec::vec::BitVec;
use derive_new::new;
use itertools::Itertools;
use log::debug;
use rustc_hash::FxHashMap;
use crate::errs::MkResult;
use crate::fasta::MotifLocationsLookup;
use crate... |
b1d380c4177d2e8e947ff0272af563ef803b050f754ee7db5ff18f9aa8cdf8d1 | Rust | 24,445 | 808 | use std::collections::{BTreeMap, HashMap};
use std::fmt::{Display, Formatter};
use std::path::PathBuf;
use anyhow::{anyhow, bail, Context, Result as AnyhowResult};
use derive_new::new;
use indicatif::{MultiProgress, ProgressIterator};
use itertools::Itertools;
use log::{debug, info};
use rayon::prelude::*;
use regex::... |
b71feaaa537284e6b582b8384f5ecc30c67827f6679b8d2d8d63fbbc4d0aae25 | Rust | 28,956 | 794 | use std::cmp::Ordering;
use std::collections::{HashMap, HashSet};
use std::fs::File;
use std::io::{stdout, BufRead, BufReader, BufWriter, Write};
use std::path::{Path, PathBuf};
use anyhow::{anyhow, bail, Context};
use bigtools::{
beddata::BedParserStreamingIterator, BigWigWrite, InputSortType,
};
use clap::{Args,... |
2722985e5f3c78dacba438c2dd883249f46c078c7581d78848f1ce7511c8a726 | Rust | 30,204 | 892 | use anyhow::bail;
use std::fmt::{Display, Formatter};
pub(crate) mod nt_bytes {
pub const A: u8 = 65;
pub const C: u8 = 67;
pub const G: u8 = 71;
pub const T: u8 = 84;
pub const BASES: [u8; 4] = [A, C, G, T];
}
pub(super) mod iupac_offsets {
const A: usize = 0;
const C: usize = 1;
cons... |
fe3673442ba0d90e6976b360d5df68ef0822800bc80734687f462b089e4531e3 | Rust | 31,237 | 1,018 | use anyhow::Context;
use itertools::Itertools;
use rust_htslib::bam;
use std::cmp::Ordering;
use std::collections::HashMap;
use std::fs::File;
use std::io::{BufRead, BufReader};
use std::path::PathBuf;
use common::{check_against_expected_text_file, run_modkit};
use mod_kit::dmr::bedmethyl::BedMethylLine;
use mod_kit::... |
73958a357e204ffaa7245ca3685f20238e6d4f4be5fcbaa30a711e68b7056583 | Rust | 32,299 | 868 | use crate::errs::{MkError, MkResult};
use crate::extract::args::InputArgs;
use crate::interval_chunks::{
ReferenceIntervalBatchesFeeder, TotalLength, WithPrevEnd,
};
use crate::mod_bam::{CollapseMethod, EdgeFilter, TrackingModRecordIter};
use crate::mod_base_code::ModCodeRepr;
use crate::monoid::Moniod;
use crate::... |
63ced8367b8c7a0ae5dcdc9d4b3db8570715979673034ab4506f04a5ade42d49 | Rust | 34,131 | 956 | use anyhow::{anyhow, bail};
use bitvec::{order::Lsb0, view::BitView};
use derive_new::new;
use memchr::{memchr, memchr_iter};
use rust_htslib::bam::{
self,
ext::{BamRecordExtensions, IterAlignedPairs},
record::AuxArray,
};
use crate::{
errs::MkResult,
mod_base_code::{DnaBase, ModCodeRepr},
util... |
9e43b1bfa8be7d60828700d522d867d5c8cd760d19c46c3b44a690b4630307ab | Rust | 40,080 | 1,072 | use std::cmp::Ordering;
use std::collections::{HashMap, HashSet, VecDeque};
use std::fmt::{Display, Formatter};
use std::ops::Range;
use std::path::{Path, PathBuf};
use anyhow::{anyhow, bail, Context};
use derive_new::new;
use indexmap::IndexSet;
use indicatif::{MultiProgress, ProgressIterator};
use itertools::Itertoo... |
faeca1505239b134ec1422a47f2054b655e0f448cc9d296ce575d8abaef3fa98 | Rust | 40,310 | 1,134 | use std::cmp::Ordering;
use std::collections::{BTreeMap, HashMap, HashSet};
use std::fmt::{Debug, Display, Formatter};
use std::fs::File;
use std::io::{BufRead, BufReader, Write};
use std::path::PathBuf;
use std::string::FromUtf8Error;
use ansi_term::Style;
use anyhow::{anyhow, bail};
use clap::Args;
use derive_new::n... |
f4b2c64d4516d44afe932ad306354f88ae22b5cf0ea4d1eb0075d6c3ebd142cb | Rust | 40,901 | 1,131 | use std::collections::HashMap;
use std::path::PathBuf;
use std::sync::RwLock;
use anyhow::{anyhow, bail, Context};
use clap::{Args, Subcommand};
use common_macros::hash_map;
use indicatif::{MultiProgress, ParallelProgressIterator};
use itertools::Itertools;
use log::{debug, info};
use prettytable::{row, Table};
use ra... |
8b1e1449d605fa76da6bc40dfaa2b974b9abf7cc9590d35783383cff411daa45 | Rust | 44,458 | 1,196 | use itertools::Itertools;
use rustc_hash::FxHashMap;
use std::collections::{HashMap, HashSet};
use std::path::{Path, PathBuf};
use anyhow::{bail, Context};
use clap::{Args, Subcommand};
use common_macros::hash_map;
use crossbeam_channel::bounded;
use indicatif::{MultiProgress, ProgressIterator};
use log::{debug, error... |
cd378f152382a18351aab6df344bdf9057fbdf373476226e4b9c6830370d9923 | Rust | 45,748 | 1,347 | use std::cmp::Ordering;
use std::collections::{BTreeMap, BTreeSet, HashMap, VecDeque};
use std::fs::File;
use std::io::{BufWriter, Write};
use std::ops::Range;
use std::path::PathBuf;
use std::sync::Arc;
use anyhow::bail;
use derive_new::new;
use indicatif::{MultiProgress, ProgressBar};
use itertools::Itertools;
use l... |
e047ade7ab773d065bdd744ba5222f66c12c3bf372bdbe513263ca7776644243 | Rust | 47,992 | 1,518 | use std::cmp::Ordering;
use std::collections::{HashMap, HashSet};
use std::fmt::{Debug, Display, Formatter};
use std::hash::Hash;
use std::io::{BufRead, BufReader};
use std::path::{Path, PathBuf};
use std::str;
use anyhow::{anyhow, bail};
use anyhow::{Context, Result as AnyhowResult};
use bio::alphabets::dna::compleme... |
baf4424ddb418b470e2b23a8c635c9fb554762feaa3c98c266dfb085462fa87c | Rust | 49,863 | 1,375 | use std::collections::{BTreeMap, HashMap, HashSet};
use std::ops::ControlFlow;
use bio::alphabets::dna::revcomp;
use derive_new::new;
use indicatif::ParallelProgressIterator;
use itertools::Itertools;
use log::debug;
use rayon::prelude::*;
use rust_htslib::bam::ext::BamRecordExtensions;
use rust_htslib::bam::record::C... |
f6d529a063299cffacd290b29a4cab5fdf2785b692cbc1d3be7d8f17da9c6df9 | Rust | 51,031 | 1,475 | use std::cmp::Ordering;
use std::collections::{BTreeMap, HashMap};
use std::fs::File;
use std::io::{stdout, BufWriter, Cursor, Stdout, Write};
use std::path::{Path, PathBuf};
use anyhow::{anyhow, bail, Context, Result as AnyhowResult};
use bitvec::order::Lsb0;
use bitvec::view::BitView;
use charming::component::{
... |
4af3f4b65ddba7555e1e4c8f4a65e68753c2e98351908c37ebfb7c502a84a2fd | Rust | 60,438 | 1,695 | use std::collections::{BTreeSet, HashMap, HashSet, VecDeque};
use std::fs::File;
use std::io::{BufRead, BufReader};
use std::ops::Range;
use std::path::PathBuf;
use std::sync::Arc;
use anyhow::{anyhow, bail, Context};
use derive_new::new;
use itertools::{Itertools, MinMaxResult};
use log::{debug, info};
use nom::chara... |
877e157d9f39709eb71f3302a6990ebce951728f4eac40c34ead0e2dc69c7136 | Rust | 62,076 | 1,761 | use std::{
collections::HashMap, marker::PhantomData, path::PathBuf, sync::Arc, usize,
};
use anyhow::{anyhow, bail};
use bitvec::{order::Lsb0, view::BitView};
use derive_new::new;
use indicatif::MultiProgress;
use itertools::Itertools;
use log::{debug, info, warn};
use log_once::{debug_once, warn_once};
use prett... |
42c78e5c3cdee5a231660e5ea652e928443c10db7e70819161edd3a829c9af94 | Rust | 75,615 | 1,940 | use std::collections::{BTreeMap, HashMap, HashSet};
use std::fs::File;
use std::io::{BufRead, BufReader, BufWriter, Write};
use std::ops::Neg;
use std::path::{Path, PathBuf};
use std::sync::Arc;
use anyhow::{anyhow, bail, Context};
use clap::{Args, Subcommand};
use indexmap::IndexMap;
use indicatif::{MultiProgress, Pr... |
8d1d938d22ac862cfbc250d1d9ff4ba30b3d99824e5d5d80d533a215e01d465c | Rust | 83,338 | 2,597 | use std::{
collections::{HashMap, HashSet},
fmt::{Debug, Write},
fs::File,
io::{BufRead, BufWriter, Write as IoWrite},
ops::Neg,
path::{Path, PathBuf},
sync::Arc,
};
use crate::{
dmr::isoform::{
gtf_reader::open_gtf_reader,
pair::run_gene_dmr,
scoring::{dirichlet... |
2e9fde9991373abe6edbe143f0daae292c5636faa66eddf970792f725fd4b7c3 | Rust | 87,827 | 2,509 | use std::{
cmp::Ordering, collections::HashMap, marker::PhantomData, ops::Range,
path::PathBuf,
};
use anyhow::{anyhow, bail};
use bitvec::slice::BitSlice;
use common_macros::hash_map;
use itertools::Itertools;
use rustc_hash::{FxHashMap, FxHashSet};
use std::ops::BitOrAssign;
use crate::{
errs::{MkError,... |
ed28075b62c58c1e26be4f1a5dd6e9dfd816d9836e7142e606c8404d324d04ac | Rust | 95,499 | 2,377 | use std::collections::{BTreeMap, BTreeSet, HashMap, HashSet};
use std::io::BufWriter;
use std::path::{Path, PathBuf};
use std::sync::Arc;
use anyhow::{anyhow, bail, Context};
use clap::Args;
use common_macros::hash_set;
use crossbeam_channel::bounded;
use indicatif::{MultiProgress, ParallelProgressIterator};
use itert... |
bb63958f35b468ac36c829c27fbe10cc53d09226095670f174d3370b73affe9f | Rust | 99,212 | 2,475 | use std::collections::{BTreeMap, BTreeSet, HashMap, HashSet};
use std::num::ParseFloatError;
use std::ops::AddAssign;
use std::path::{Path, PathBuf};
use std::sync::Arc;
use anyhow::{anyhow, bail, Context};
use clap::{Args, Subcommand, ValueEnum};
use indicatif::{MultiProgress, ParallelProgressIterator, ProgressDrawTa... |
6a7a7f91ef9531bb7120b8ecd8adc95189927f3dbae5ccf995772e8fa137de0a | Rust | 101,441 | 2,919 | use std::cmp::Ordering;
use std::collections::{HashMap, HashSet};
use std::fmt::{Debug, Display, Formatter};
use std::hash::Hash;
use anyhow::bail;
use derive_new::new;
use itertools::{Itertools, PeekingNext};
use log::debug;
use nom::bytes::complete::tag;
use nom::character::complete::{digit1, multispace0};
use nom::... |
985bd0f03a4e88e1f554836fa67828e04137a73fd4279c5d173b96a9dc4b4f65 | Rust | 124,555 | 3,651 | use std::cmp::Ordering;
use std::collections::{BTreeMap, HashMap};
use std::fmt::{Display, Formatter};
use std::io::{BufRead, BufReader};
use std::ops::Range;
use std::path::PathBuf;
use std::sync::{Arc, RwLock};
use anyhow::{anyhow, bail, Context};
use bitvec::prelude::*;
use derive_new::new;
use indicatif::{MultiPro... |
877ff8bc6565fd0a32042267f8a893c1ac6191d7643cd1a89673350ec9edd266 | Shell | 35 | 2 | #!/bin/bash
pip install rdkit-pypi
|
cb2ce8dfefb1c940fd612d0534d0cd65f509121210cca9056bcf377692c47c37 | Shell | 115 | 3 | #!/bin/sh
python custom/download_script.py
python custom/task_execution.py --queue "custom-cpu" --concurrency "$1"
|
db05b755940751d385fe420a9e127605b2f2f1a31af8d210aec8375341668c70 | Shell | 115 | 3 | #!/bin/sh
python custom/download_script.py
python custom/task_execution.py --queue "custom-gpu" --concurrency "$1"
|
41f8abc12ca5a20d69bc75d4df27b2ce4d86f32d577e46aa059b3a5a1f90296c | Shell | 116 | 7 | set -e
rm -rf docs/generated/
black .
isort .
ruff .
coverage run -m unittest
sphinx-build -W docs docs/_build/html
|
334f7ba68de9f01151e6df8061249e29b9c5a53f3159891076e5bb7f92f79231 | Shell | 122 | 1 | $PYTHON setup.py install --single-version-externally-managed --record=record.txt # Python command to install the script.
|
dae5b9c6184dde7fde86e40279359a2395c1f8409fd82d829791ab073991ee04 | Shell | 137 | 6 | #!/usr/bin/env bash
set -euo pipefail
for b in 1 2 3 4; do
bash scripts/02_run_batch.sh "$b"
done
bash scripts/04_check_bam_outputs.sh
|
a418ea9202a8232346f40695140fe32169bf3356affb660a84b5a46ba72d6989 | Shell | 152 | 1 | docker run -d -p 1111:8787 -e USER=user -e PASSWORD=pw --name rstudio_docker -v /data/to/mount/:/home/user/data jsschrepping/r_docker:jss_R432_bioc318
|
2442cf1f2197a51f6d44694755c8f085879851e21528c8f9b96f090a4b9692ae | Shell | 172 | 8 | #!/usr/bin/env bash
set -euo pipefail
if grep -n '^RUN_TESTS_.*=0' tests/*.sh; then
echo "Found disabled RUN_TESTS_ in test scripts. Set them to '=1'."
exit 1
fi
|
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