sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2c9f5bdb9e69caf19c70542a22328905ddf862a1c747f8551ba933642eed706a | Rust | 14,152 | 403 | // This file is @generated by prost-build.
#[derive(Clone, PartialEq, Eq, Hash, ::prost::Message)]
pub struct AnnotationFeature {
/// chain type of the reference record, e.g. TRA
#[prost(enumeration = "VdjChain", tag = "1")]
pub chain: i32,
/// same as gene_name
#[prost(string, tag = "2")]
pub d... |
98f563d084fc5aaa97a90e4ce8ba810e5e6ecf0a920d5561af20239d53f8d3e9 | Rust | 14,402 | 348 | //! Martian stage GENERATE_CAS_WEBSUMMARY
//! Dump vega plots into cell annotation websummary
#![deny(missing_docs)]
use crate::HtmlFile;
use crate::cell_annotation_ws_parameters::{
CellAnnotationMetrics, CellTypeWebSummaryBundle, CellTypeWebSummaryBundleValue,
WebSummaryCellTypeInputs, generate_cas_bc_mismatch... |
af8b707510d3bdc20cc91d95b0687d6d269edc290b9f9f5d3c9897064749681f | Rust | 14,412 | 419 | //! Reading/Writing the vdj contig proto file which is used for VDJ aggr. This file contains
//! metadata about the VDJ analysis, the VDJ reference and a list of annotated contigs.
//!
//! The messages are defined in `types.proto`. The file format is as follows
//! ```text
//!
//! +-------------------------+
//! | Numb... |
a5775fe02afb273535dc31a02bd88ccded12a735a9509e01f094be3f3fb4ef0d | Rust | 14,634 | 514 | #![deny(missing_docs)]
use nom::branch::alt;
use nom::bytes::complete::{tag, take_till};
use nom::character::complete::char;
use nom::combinator::peek;
use nom::error::{ErrorKind, make_error};
use nom::multi::{many_till, many0, many1};
use nom::sequence::{delimited, preceded, terminated};
use nom::{Err, IResult, InputT... |
20f6de81423efca9dfdefddd637aa52fa7b55413639c9ace0b4e99467c849f44 | Rust | 14,704 | 348 | //! Filter B cells based on UMI counts.
// Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#![deny(missing_docs)]
use crate::core::barcode_fate::BarcodeFate;
use crate::core::defs::{CloneInfo, EncloneControl, ExactClonotype};
use crate::core::enclone_structs::{BarcodeFates, CandidateClonotype};
use itertool... |
46a0973c07a213073f5856be7fcd41b3af0a21db40e5bb9c1b4d3787c9d5c4b6 | Rust | 14,878 | 405 | #![expect(missing_docs)]
use crate::constants::UmiType;
use bio;
use bio::alignment::{Alignment, AlignmentOperation};
use lazy_static::lazy_static;
use serde::{Deserialize, Serialize};
use std::cmp;
pub type Scoring = bio::alignment::pairwise::Scoring<bio::alignment::pairwise::MatchParams>;
const MAX_OUT_QUAL: u8 = 60... |
4f4e7eef71bc295031bd816c3213a7967eb38158a10a0527395283bf940c8a79 | Rust | 14,888 | 383 | #![expect(missing_docs)]
use crate::constants::{ReadType, UmiType};
use crate::sw;
#[cfg(test)]
use crate::{bam_utils, utils};
use debruijn::dna_string::DnaString;
#[cfg(test)]
use rust_htslib::bam;
use serde::{Deserialize, Serialize};
/// A macro creating methods for flag access.
/// Copied from rust_htslib.
macro_ru... |
d2b77fbb217e2d87256fb0af4a9d90f1aafdb273b68ba633a2ddf5c2f17de136 | Rust | 14,938 | 445 | //! Martian stage MULTI_PREFLIGHT
//! Run pre-flight checks.
#![deny(missing_docs)]
use crate::MultiParams;
use crate::preflight::{
check_crispr_target_genes, check_resource_limits, check_vdj_inner_enrichment_primers,
check_vdj_known_enrichment_primers, hostname, validate_target_panel,
};
use anyhow::{Context,... |
deab223caec537c8c493f542e0b450ff6a5d6799843084cf34a368320f979b0b | Rust | 15,354 | 429 | //! Identify duplicate reads originating from the same molecule.
#![expect(missing_docs)]
use crate::read::{AnnotationInfo, ReadAnnotations, RecordAnnotation};
use bytes::Bytes;
use cr_types::probe_set::ProbeSetReference;
use cr_types::reference::feature_reference::FeatureReference;
use cr_types::rna_read::RnaChunk;
u... |
4e82aed4e5455ba0388f463d178bca25cb19ef4e0a846268f2cd7b6af97dd1c8 | Rust | 15,387 | 419 | //! Martian stage WRITE_BARCODE_SUMMARY
//! Write the file barcode_summary.h5.
#![deny(missing_docs)]
use crate::BarcodeMetricsShardFile;
use crate::align_metrics::{
BarcodeKind, BarcodeMetrics, GenomeMapping, LibFeatThenBarcodeOrder, MULTI_GENOME,
MappingRegion,
};
use crate::utils::estimate_mem::barcode_mem_... |
7a9bd03e8eb148a93e6e908b7a8688276d1895b1d80f674a20db4a5b5a1febea | Rust | 15,489 | 411 | //! Martian stage BUILD_PER_SAMPLE_VDJ_WS_CONTENTS
#![deny(missing_docs)]
use crate::SequencingMetricsFormat;
use crate::stages::parse_multi_config::VdjGenInputs;
use anyhow::Result;
use cr_types::{
BarcodeMultiplexingType, CellLevel, CrMultiGraph, LibraryType, MetricsFile, ReadLevel,
SampleAssignment, Sequenc... |
1121846b3a3a4e8081ec183ea76d77001f1ff3e6a372ceafaa6a3490d565f4da | Rust | 15,757 | 568 | //! cr_websummary
#![expect(missing_docs)]
mod alert;
pub mod multi;
mod value;
pub use alert::{AlertContext, AlertLevel, AlertSpec};
extern crate self as cr_websummary;
use alert::Alert;
use anyhow::Result;
use metric::{PercentMetric, TxHashMap};
use plotly::Layout;
use plotly::common::Anchor;
use plotly::layout::{... |
bdc7a3ab0e6a849d4cef81ab92f36d11ec6178278d11d0fb3a086a289ca02800 | Rust | 15,839 | 377 | // Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#![deny(missing_docs)]
// This file provides the single function graph_filter.
use super::BarcodeFilter;
use crate::core::barcode_fate::BarcodeFate;
use crate::core::defs::BarcodeContigs;
use graph_simple::GraphSimple;
use io_utils::fwriteln;
use petgraph:... |
7e6fff3957f40ea46943cb0981d9c1a0071b506451f61a8e5ed1e582757205a4 | Rust | 16,025 | 434 | // Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#![deny(missing_docs)]
use crate::core::defs::{CloneInfo, EncloneControl, ExactClonotype, PotentialJoin};
use crate::core::join_one::join_one;
use equiv::EquivRel;
use qd::Double;
use std::cmp::max;
use std::collections::HashMap;
use vdj_ann::refx::RefData;... |
afe24dfcfa96670d88c8e360eb30e6ec1015305942b561fe1cf978f81dc8bb6d | Rust | 16,065 | 461 | #![deny(missing_docs)]
use anyhow::{Result, anyhow};
use core::iter::IntoIterator;
use cr_types::in_flight::{InFlightPool, Reservation};
use cr_types::spill_vec::SpillVec;
use crossbeam_channel::unbounded;
use crossbeam_utils::thread::{Scope, ScopedJoinHandle};
use itertools::Itertools;
use martian_filetypes::LazyFile... |
e4953462562dca3827ff10d7b1b55445e10cc893b1a42f42296b513dd7ab891a | Rust | 16,120 | 383 | #![expect(missing_docs)]
use crate::{ChartWithHelp, PlotlyChart, RawChartWithHelp, TitleWithHelp};
use cr_types::{GenomeName, LibraryType, TargetingMethod};
use metric::{AsMetricPrefix, TxHashMap, TxHashSet};
use plotly::Layout;
use plotly::common::{Anchor, Line, Mode};
use plotly::layout::{Axis, HoverMode, Legend, Mar... |
d7265db68add51e51024522423c155d565d2e3e08a4635eeb6498bfc0a6d8d80 | Rust | 16,421 | 458 | #![expect(missing_docs)]
use crate::config::csv::CsvParser;
use crate::config::parse::{Parse, ParseCtx};
use crate::config::scsv::{Section, Span, XtraData, plain_csv};
use crate::config::{Ident, MultiConfigCsv, SampleBarcodeColumn, multiconst};
use anyhow::{Context, Result, anyhow, bail, ensure};
use cr_types::{Barcode... |
111cc45e2126b12e5c37ddf6e329fb74cdc10ea851619be392b30ea95bdc86ac | Rust | 16,446 | 504 | // Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#![expect(missing_docs)]
use debruijn::dna_string::DnaString;
use itertools::Itertools;
use martian_derive::MartianStruct;
use martian_filetypes::json_file::JsonFile;
use serde::{Deserialize, Serialize};
use std::cmp::Ordering;
use vdj_ann::annotate::{Annot... |
5eb1759d6ab96d53ae8cadb046262c41f08383c1eec56f550808bccd27d74b68 | Rust | 16,509 | 466 | //! Martian stage COLLATE_METRICS
//! This stage receives per barcode metrics from ALIGN_AND_COUNT and creates the summary JSON.
#![deny(missing_docs)]
use crate::AggregateBarcode;
use crate::align_metrics::{BarcodeKind, BarcodeMetrics, LibFeatThenBarcodeOrder, VisitorMetrics};
use crate::types::BarcodeMetricsShardFile... |
70d4cd3845b6fd014e1e7f784b349b35dd9ebe1f9f2e2661d5aadcbdf74ce97f | Rust | 16,569 | 485 | //! Utilities for finding groups of FASTQ produced by `bcl2fastq` from Illumina.
#![expect(missing_docs)]
use crate::filenames::{LaneMode, LaneSpec};
use crate::read_pair_iter::FastqSet;
use anyhow::{Context, Result};
use itertools::Itertools;
use lazy_static::lazy_static;
use regex::Regex;
use serde::{Deserialize, Se... |
0bbe145171ffa37a8e140c7f07d90457986dfba7ee606ae89fc2556753346ee1 | Rust | 16,700 | 456 | //! Probe set reference CSV
#![deny(missing_docs)]
use crate::probe_set::{Probe, ProbeRegion, ProbeType};
use crate::reference::feature_reference::get_genome_from_feature_id;
use crate::reference::reference_info::ReferenceInfo;
use crate::{FeatureID, FeatureName};
use anyhow::{Context, Result, bail, ensure};
use itert... |
b989d166d35fb8f152b50313bcbac0e200fbb621be9a7c41c37ca75a68e73e7c | Rust | 16,811 | 541 | // Copyright (c) 2021 10x Genomics, Inc. All rights reserved.
#![expect(missing_docs)]
// This file contains functions that take as input an amino acid reference sequence for a V
// segment, along with its chain type (IGH, IGK, IGL, TRA or TRB), and attempt to find features in
// the sequence.
//
// These functions ca... |
3ef69ef7909c2996a397da9fd717c70c52f8f61196ffa61155e671ce573bf5ed | Rust | 16,965 | 539 | #![expect(missing_docs)]
use anyhow::{Context, Result, bail};
use cr_types::reference::feature_reference::{
FeatureDef, FeatureReference, FeatureType, REQUIRED_FEATURE_TAGS, TargetSet,
};
use fastq_set::read_pair::WhichRead;
use hdf5::Group;
use hdf5::types::FixedAscii;
use itertools::Itertools;
use std::borrow::Co... |
070e5621c1a07db980fe522c91ad5fab5f4a068c42a42b581e8dcbda603aca43 | Rust | 17,061 | 476 | //! Souporcell source code
//!
//! MIT License
//!
//! Copyright (c) 2019 Haynes Heaton
//!
//! Permission is hereby granted, free of charge, to any person obtaining a copy
//! of this software and associated documentation files (the "Software"), to deal
//! in the Software without restriction, including without limita... |
74ed131e3a1a14a68c4545c160f117cebc0627e6fe3096dc48d8256b8d21e5b9 | Rust | 17,932 | 469 | // Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#![deny(missing_docs)]
//
// This set of functions writes a protobuf data structure that
// Loupe uses to access clonotype data.
use self::refx::RefData;
use crate::core::defs::{AltRef, ColInfo, EncloneControl, ExactClonotype};
use crate::core::join_one::{R... |
bc9e26c40ffa757e3b44c56ab6532cab4a49b130371ad590af3119345819629c | Rust | 17,981 | 578 | use crate::aggregation::GeneAggregation;
use anyhow::{bail, Result};
use csv::ReaderBuilder;
use ndarray::{Array1, Array2, Axis};
use regex::Regex;
use std::collections::{HashMap, HashSet};
use std::{
fs::File,
io::{BufRead, BufReader},
};
type Record = HashMap<String, String>;
pub struct SimpleFrame {
he... |
a51a70ec6c80dbc3c470a4d28eb621151e39d867e9e8970c0288539f327086fc | Rust | 18,525 | 538 | //! I/O HDF5 helper functions
#![deny(missing_docs)]
use crate::types::{
ClusteringKey, ClusteringResult, ClusteringType, EmbeddingResult, EmbeddingType, H5File,
PcaResult, ReductionType, clustering_key,
};
use anyhow::{Context, Result};
use cr_types::reference::feature_reference::FeatureType;
use itertools::F... |
110293cfb244c52a7ef3689228739a0638184474a70524b57284488ba6bd643e | Rust | 18,702 | 469 | //! Martian stage DETECT_VDJ_RECEPTOR
#![deny(missing_docs)]
use crate::detect_chemistry::chemistry_filter::detect_chemistry_units;
use anyhow::{Context, Result, anyhow, bail};
use cr_types::reference::feature_reference::{BeamMode, FeatureConfig, FeatureReferenceFile};
use cr_types::sample_def::SampleDef;
use cr_types... |
b8d18cba6cc7ec51ddb61780594eee96008447ab4c6d8eff08dd79470869d773 | Rust | 19,263 | 596 | // Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
//! See README for documentation.
#![deny(missing_docs)]
use crate::Dataset;
use crate::core::barcode_fate::BarcodeFate;
use crate::core::defs::{AltRef, CloneInfo, EncloneControl};
use crate::core::enclone_structs::{BarcodeFates, CandidateClonotype, Enclone... |
eaf211b0747cd542e3a7a4f5d142ccce7835348b30b3dbdd07539c01bef7c40a | Rust | 19,464 | 541 | // Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#![deny(missing_docs)]
use self::annotate::Annotation;
use self::refx::RefData;
use crate::core::barcode_fate::BarcodeFate;
use crate::core::defs::{BarcodeContigs, Contig, EncloneControl};
use crate::core::enclone_structs::BarcodeFates;
use crate::enclone::... |
332a1001ebeb81351bfb2ec9b830c6006dcc0b3f656c8d838218a597adf564aa | Rust | 19,793 | 440 | //! Martian stage WRITE_CONTIG_OUTS
#![expect(missing_docs)]
use crate::BarcodeDataBriefFile;
use crate::assembly_types::{FastaFile, FastqFile};
use anyhow::Result;
use cr_types::MetricsFile;
use json_report_derive::JsonReport;
use martian::prelude::*;
use martian_derive::{MartianStruct, make_mro, martian_filetype};
u... |
d64539f19b3ae8419d6c25c124a8c4b4182e808b1e380e5b2dae1c15a0b8bddf | Rust | 19,854 | 526 | //! - Converting from crate::types to vdj_types
//! - Additional functions to auto derived structs
#![expect(missing_docs)]
use crate::types::vdj_proto_message::MessageContent;
use crate::types::{
AsmData, GexData, MetricsSummary, VdjMetadata, VdjProtoMessage, VdjReferenceRaw,
};
use anyhow::Result;
use itertools:... |
07a0c38aa73fb57be9bf6ae589a16694093a4e3256ea8bd493d26c7fc13f0e6c | Rust | 20,133 | 491 | // Copyright (c) 2020 10X Genomics, Inc. All rights reserved.
#![deny(missing_docs)]
// This file provides functions to find alternate alleles and substitute them into references.
use self::refx::RefData;
use crate::core::defs::{AltRef, CloneInfo, ExactClonotype};
use crate::core::join_one::REF_V_TRIM;
use debruijn::... |
ac3e615cf1abf67078f15860c6904f88a31407652e7548a9a63a9c1b1ff2ef24 | Rust | 20,345 | 486 | #![deny(missing_docs)]
use crate::fit_piecewise_linear_model::{EstimatedModel, PiecewiseLinearData};
use crate::probe_barcode_matrix::ProbeCounts;
use anyhow::Result;
use barcode::Barcode;
use cr_h5::molecule_info::MoleculeInfoIterator;
use cr_types::probe_set::{ProbeRegion, ProbeSetReference};
use cr_types::reference:... |
06d9eeae56d73f798e0a3e9748c5fc01ccc9594bfa27548651da8d18637330e5 | Rust | 20,372 | 569 | //! Martian stage WRITE_POS_BAM
#![deny(missing_docs)]
use crate::{BamFile, env};
use anyhow::{Result, bail};
use barcode::Barcode;
use cr_bam::bam::{BamPosSort, estimate_memory_for_range_gib};
use cr_types::rna_read::{RnaChunk, make_library_info};
use cr_types::types::{SampleAssignment, SampleBarcodes};
use cr_types:... |
93e13bac531d0413b315a5d8cbd3852717fed3c9887d6fdb4495155a3fa7ca5b | Rust | 20,547 | 610 | //! Process a specification file into a metrics ETL operation.
//!
//! ETL = Extract, Transform, Load
//! In this case, we extract metrics from the pipestance scope, transform their
//! data types and process possible alerts, then load them into output data
//! structures.
#![deny(missing_docs)]
use super::websummary:... |
c4ea51fb0b1143c294f02635260812089278be428bcf1af780af6380a184e755 | Rust | 20,761 | 562 | #![expect(missing_docs)]
use crate::Gene;
use crate::parse_gtf::{parse_gtf_line, validate_gtf_line};
use anyhow::{Context, Result, anyhow, bail, ensure};
use bio::io::fasta::IndexedReader;
use bio_types::strand::ReqStrand;
use flate2::read::MultiGzDecoder;
use std::collections::hash_map::Entry;
use std::collections::{B... |
3bee33c854ca823a59cf0c0c33e21132f8e85cb479454482a4a771a7f88244be | Rust | 21,047 | 575 | // Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#![deny(missing_docs)]
use super::defs::{CloneInfo, EncloneControl, ExactClonotype, PotentialJoin};
use debruijn::Mer;
use debruijn::dna_string::ndiffs;
use itertools::zip_eq;
use qd::{Double, dd};
use std::cmp::min;
use std::collections::HashMap;
use strin... |
08b59db21d55331ae11c12e8e8c47ccdee2b018cac5c1bdd852b9cda700c3612 | Rust | 21,094 | 514 | //! Martian stage CHECK_BARCODES_COMPATIBILITY_VDJ
#![deny(missing_docs)]
use super::sample_valid_barcodes;
use anyhow::{Result, ensure};
use barcode::BcSegSeq;
use cr_types::chemistry::{ChemistryDef, ChemistryDefs, ChemistryName};
use cr_types::sample_def::SampleDef;
use cr_types::{ERROR_CODE_INFO, LibraryType};
use ... |
da7b07737521b0071e94732d9fae2adbad60cb949f60ccbd6ff98ca3f29a1406 | Rust | 21,179 | 547 | #![deny(missing_docs)]
use crate::SequencingMetrics;
use crate::barcode_sort::ReadTrimmingMetrics;
use anyhow::Result;
use barcode::{BarcodeConstruct, BarcodeConstructMetric, BcSegSeq};
use cr_types::SequencingPlatform;
use cr_types::chemistry::ChemistryDef;
use cr_types::reference::feature_extraction::FeatureExtracto... |
6cbbc4de0c5bb519e1d744f2f86b43c09c6bd023a11a2dc404ef663bb9d0f6f6 | Rust | 21,263 | 603 | #![expect(missing_docs)]
///
/// Types for dealing with 10x barcodes
///
use crate::{LibraryType, hardlink_with_fallback};
use anyhow::{Result, format_err};
use barcode::Barcode;
use itertools::Itertools;
use martian::{AsMartianBlanketType, AsMartianPrimaryType, MartianBlanketType};
use martian_derive::{MartianStruct, ... |
79f27eddeed34d413af27e22dcca905be8676305dddad814a5831041a4dfc20b | Rust | 22,731 | 623 | //! Martian stage MERGE_MOLECULES
#![expect(missing_docs)]
use anyhow::Result;
use barcode::BarcodeContent;
use cr_h5::molecule_info::{
BarcodeIdxType, LibraryIdxType, MoleculeInfoIterator, MoleculeInfoReader, MoleculeInfoWriter,
bin_barcodes, open_for_modification, trim_barcodes,
};
use cr_types::aggr::CountA... |
36fc9768abfda3be095f41693e92b5f6a971a0e178ea5a3cf353dba240fa505e | Rust | 22,868 | 717 | // Copyright (c) 2018 10x Genomics, Inc. All rights reserved.
#![expect(missing_docs)]
//! Sized, stack-allocated container for a short DNA sequence.
use crate::array::{ArrayContent, ByteArray};
use itertools::Itertools;
use std::iter::Iterator;
use std::str;
const UPPER_ACGTN: &[u8; 5] = b"ACGTN";
const N_BASE_INDE... |
b5baa1962ccbb4c95628a35145ef75e4bc17128bdc4fdb5f935629841d7c7190 | Rust | 23,237 | 657 | //! A hacked-up version of the aligner from rust-bio to allow injecting custom
//! scoring penalties.
// Copyright 2014-2015 Johannes Köster, Vadim Nazarov, Patrick Marks
// Licensed under the MIT license (http://opensource.org/licenses/MIT)
// This file may not be copied, modified, or distributed
// except according t... |
32b69c55239f213e420146d60ce178140cfadd38434095abc898205b9063a467 | Rust | 23,730 | 653 | #![expect(missing_docs)]
use crate::filter_log::{AsmCellFilter, FilterLogEntry, FilterLogger, LowConfidenceReason};
use crate::pack_dna::pack_bases_80;
use anyhow::Result;
use arrayref::array_ref;
use barcode::BcSegSeq;
use barcode::whitelist::BarcodeId;
use bio::alignment::distance::simd::hamming;
use cr_types::chemis... |
6d23219eafe79b7617ae6fbaa48c3195785ddff68094c35de1788f03a1814fdb | Rust | 24,033 | 704 | #![expect(missing_docs)]
use crate::rna_read::AdapterTrimmingParameters;
use crate::{AlignerParam, LibraryType};
use anyhow::{Ok, Result, bail, ensure};
use fastq_set::SSeq;
use fastq_set::filenames::bcl_processor::SampleIndexSpec;
use fastq_set::filenames::bcl2fastq::{self, SampleNameSpec};
use fastq_set::filenames::f... |
3c558e392848c8c073f206f7b4cf85cd5d6538309657378297460bb6ab57fccf | Rust | 24,220 | 588 | //! Martian stage CHECK_BARCODES_COMPATIBILITY
//!
//! This stage checks that barcodes from different libraries are compatible.
//!
//! ## What is the meaning of compatibility?
//!
//! A set of cells processed through a single 10x gem well could be used to create multiple sequencing
//! libraries (GEX, Ab etc.). In ord... |
16ab7fc6edefb8af010588d55708d81caeaf91a0e740e3f4456faab315112d43 | Rust | 24,697 | 633 | //! hyperbase
// Copyright (c) 2018 10X Genomics, Inc. All rights reserved.
#![expect(missing_docs)]
// This file defines a HyperBasevector structure, and a Hyper structure, which
// is a HyperBasevector plus an involution and read ids for each edge.
use debruijn::compression::{SimpleCompress, compress_kmers};
use de... |
2de9bc511e73b4853ed860601a852c0838079221e36a1f4af2c4f92c9c05ca27 | Rust | 25,167 | 517 | // This file is @generated by prost-build.
/// Evidence that a given cell is iNKT or MAIT. Each ExactSubclonotype has one
/// instantiation of this structure for iNKT and one for MAIT.
#[derive(::serde::Serialize, ::serde::Deserialize)]
#[allow(clippy::derive_partial_eq_without_eq)]
#[derive(Clone, Copy, PartialEq, :... |
74a2e34f869b5624bd576b55bbba18345a027b8d3ef49616e148a70d8cf13c01 | Rust | 25,398 | 672 | //! Martian stage COMPUTE_SUBSEQ_METRICS
//!
//! Compute distinct-subsequence metrics over cell-associated gel-bead barcodes.
#![deny(missing_docs)]
use anyhow::{Result, bail};
use barcode::{BcSegSeq, WhitelistSpec};
use cr_types::LibraryType;
use cr_types::chemistry::{BarcodeReadComponent, ChemistryDef, ChemistryDefs... |
d7ec6970f8ead69848bf58e72362b8da59b98a0815c0c54bd7c0ea5f5f55d4a6 | Rust | 25,743 | 584 | //! Martian stage SPLIT_PERTURBATION_MATRIX
//!
//! Stream the filtered feature-barcode matrix once and emit, for the two downstream
//! `MEASURE_PERTURBATIONS` instances (by-feature and by-target), everything they need WITHOUT ever
//! materializing a per-chunk feature×cell matrix:
//!
//! - **Sufficient statistics*... |
7fdbc0d1a03a43bb7f8d67c775746d559574eb9928c7e73a2cb39034f7bdaa97 | Rust | 26,141 | 689 | //! JIBES implemented in Rust, this code is a mirror of the python code in cellranger.analysis.jibes
//! with the regression and model fitting steps optimized to use significantly less memory and run
//! a lot faster. Any changes here should be reflected in the python code and vice-versa.
#![deny(missing_docs)]
use n... |
47a50f69aa9ef2a4e144fb738b5e8fd72db8648a6ad42a10c920e2f515a9675c | Rust | 26,380 | 744 | #![deny(missing_docs)]
use crate::make_shard_metrics::{MakeShardMetricProc, MakeShardMetricsAccum};
use anyhow::Result;
use barcode::{Barcode, BarcodeConstructMetric};
use cr_bam::constants::{ALN_BC_DISK_CHUNK_SZ, ALN_BC_ITEM_BUFFER_SZ};
use cr_types::chemistry::ChemistryDef;
use cr_types::rna_read::{RnaChunk, RnaProc... |
6b0fb45a46729ac71b080d6f00bab285194c8b7d58a7fdab7100467f62ecc946 | Rust | 26,726 | 673 | //! Martian stage MAKE_SHARD
#![deny(missing_docs)]
use crate::SequencingMetricsFormat;
use crate::barcode_correction_metrics::{BarcodeCorrectionMetrics, BarcodeCorrectionMetricsFormat};
use crate::barcode_sort::{BarcodeSortResults, execute_barcode_sort_with_visitor};
use crate::make_shard_metrics::{
MakeShardHist... |
62d6a553c784ee469ecb0421371a6115843c07fc3e81fb77f2a4b9b2ab4831e2 | Rust | 26,734 | 660 | //! Martian stage CALL_TAGS_READ_LEVEL
//! Assign cells to samples using their sample barcode sequence.
#![deny(missing_docs)]
use crate::barcode_overlap::{
FRPGemBarcodeOverlapRow, GelBeadBarcodesPerProbeBarcode, ProbeBarcodeGelBeadGrouper,
calculate_frp_gem_barcode_overlap,
};
use crate::detect_chemistry::pr... |
43ef90378f8ed9e22d5109dfcf4215370bbd31dbebf7410ad6f295a3e46e9aa1 | Rust | 26,774 | 913 | //! This module defines structures useful in keeping track of distributions.
//! The following structs are defined
//! * `SimpleHistogram<K>` : Histogram to keep track of counts of different items
#![deny(missing_docs)]
use crate::{CountMetric, JsonReport, JsonReporter, Metric, TxHashMap};
use itertools::Itertools;
use... |
fd8de8c56599d5fe93ad17c471f7588d77b244b181dca6c17bd26bb3b7693b46 | Rust | 27,084 | 706 | //! Martian stage WRITE_MOLECULE_INFO
#![deny(missing_docs)]
use super::parse_multi_config::CellCalling;
use crate::BcUmiInfoShardFile;
use crate::probe_barcode_matrix::ProbeCounts;
use crate::stages::SampleMetrics;
use crate::stages::parse_multi_config::CellCallingParam;
use crate::utils::estimate_mem::get_total_barc... |
a2f2eae3bced6f5a07444237ae44c0186b085cc61008b871a17b6bec7dac2101 | Rust | 27,120 | 784 | #![expect(missing_docs)]
use super::feature_reference::FeatureType;
use crate::constants::ILLUMINA_QUAL_OFFSET;
use crate::reference::feature_reference::{FeatureDef, FeatureReference};
use crate::rna_read::RnaRead;
use anyhow::{Result, anyhow, bail};
use fastq_set::read_pair::WhichRead;
use itertools::Itertools;
use re... |
ae38ee42d508ad3ba0fa1571e73de08ab4f2cfe67530fc79961eb7673b0e1d05 | Rust | 27,172 | 856 | //! This crate defines a number of data structures used for tracking
//! various metrics in a pipeline. `Metric` trait forms the core of this
//! crate and all the data structure which represents a metric implements
//! this trait. The crate `metric_derive` allows one to derive the `Metric`
//! trait. The data structur... |
b85948c1d6e57f1db382a5221137e78cbba58f90137aa51f13f17edfc2554e49 | Rust | 27,437 | 673 | //! Martian stage BARCODE_CORRECTION
#![deny(missing_docs)]
use crate::barcode_correction_metrics::{
BarcodeCorrectionMetrics, BarcodeCorrectionMetricsFormat, BarcodeDiversityMetrics,
};
use crate::barcode_sort::BarcodeOrder;
use crate::stages::make_correction_map::CorrectionMapFormat;
use crate::types::ReadShardF... |
e4e154bd407383c56702558e9d26a4bb90cd698432bce7462e14cd8c1d843825 | Rust | 28,008 | 626 | // Cell Annotation Web Summary Parameters used across multi, count, and spatial
#![deny(missing_docs)]
use anyhow::{Ok, Result};
use martian_derive::MartianStruct;
use martian_filetypes::FileTypeRead;
use martian_filetypes::json_file::JsonFile;
use metric::TxHashMap;
use serde::{Deserialize, Serialize};
use serde_json:... |
5602ed0c76625b6e3bcc2586ab410e21d000c0c8eb4011094aa74e6ca07a149a | Rust | 28,963 | 722 | #![deny(missing_docs)]
use anyhow::{Context, Result};
use diff_exp::diff_exp::{DiffExpResult, SSeqParams, sseq_de_from_sums, sseq_params_from_moments};
use diff_exp::stat::Statistics;
use diff_exp::{NbExactBackend, compute_sseq_params, sseq_differential_expression_backend};
use ndarray::Array1;
use numpy::{Element, In... |
ac5751c79a4ddc8372ef1fb0c058f7ae2504adf44b8cc01d97877ec09e7e981c | Rust | 29,378 | 853 | #![deny(missing_docs)]
use crate::align_homopolymer::count_homopolymer_matches;
use crate::minimap2::{MinimapAligner, new_record};
use anyhow::Result;
use barcode::{Barcode, BarcodeContent};
use cr_types::chemistry::ChemistryName;
use cr_types::constants::ILLUMINA_QUAL_OFFSET;
use cr_types::probe_set::ProbeSetReferenc... |
55b08e73bf9843a72c80b8a2ef8542be13b3e4e8b25be41845ad422022a3e61f | Rust | 29,773 | 868 | //! Data structure for parsing the VDJ reference and other helper function
#![expect(missing_docs)]
use anyhow::{Result, bail};
use bio::io::fasta::{self, Record};
use errors::{ErrorContext, HeaderErrors, VdjReferenceErrors};
use martian_derive::MartianType;
use serde::{Deserialize, Serialize};
use std::collections::H... |
9c07188ba1f461e6ec0915313a247daa38a7c1b14d93440f90c9df6944060ab5 | Rust | 29,960 | 811 | #![expect(missing_docs)]
use crate::binned::SquareBinRowOrColumnIndex;
use crate::{BarcodeSegment, BarcodeSegmentContent, BcSegSeq, io_utils};
use anyhow::{Context, Result, bail};
use barcodes_folder::find_whitelist;
pub use barcodes_folder::{find_atac_whitelist, find_slide_design};
use itertools::Itertools;
use martia... |
ae333e111a1a2f1dbc6e2a6bd812607a0aed2f601a74c05870a7ad1a670c9be9 | Rust | 30,722 | 820 | //! A feature-barcode count matrix.
#![expect(missing_docs)]
use crate::iter::{H5Iterator, ThreadedH5Iterator};
use crate::{
ChunkedWriter, ColumnAction, extend_dataset, feature_reference_io, make_column_ds,
scalar_attribute, write_column_ds,
};
use anyhow::{Context, Result, bail};
use barcode::{Barcode, MAX_B... |
4a5da6ebd9e33aa9aa20c959a5fe56ff7c0fd82a6f704c949217978c7b23bbc1 | Rust | 31,914 | 781 | // TODO: fix these.
#![expect(missing_docs)]
#![allow(clippy::needless_range_loop)]
use crate::filter_barcode_level::BarcodeCellInfo;
use crate::filter_log::{
AsmCellFilter, FilterLogEntry, FilterLogger, FilterSwitch, IndelErrorMode,
};
use crate::pack_dna::unpack_bases_80;
use barcode::{Barcode, BcSeq};
use debru... |
eeec9af2174b9711bf0396be2c9794d556732e377db9fc34c2993a5dc0a73453 | Rust | 32,235 | 844 | #![deny(missing_docs)]
use anyhow::{Context, Result, bail, ensure};
use bio::alphabets::dna::revcomp;
use cr_h5::probe_reference_io::PROBE_DATA_LEN;
use cr_types::probe_set::ProbeSetReferenceMetadata;
use cr_types::reference::feature_reference::{FeatureReference, FeatureType};
use cr_types::reference::probe_set_refere... |
0721dfea696c58358e6e5c483c1d3e3b9262ee61098611b32e8d2a0f3c73b9d1 | Rust | 33,091 | 956 | //! Read a set of FASTQs, convert into an Iterator over ReadPairs.
// Copyright (c) 2018 10x Genomics, Inc. All rights reserved.
#![expect(missing_docs)]
use crate::ERROR_CODE_INFO;
use crate::read_pair::{MutReadPair, ReadHeader, ReadPair, ReadPairStorage, ReadPart, WhichRead};
use anyhow::{Context, Result, anyhow, ba... |
7ee1f391d0dfcbebed5369c509a0ee5978c38ed2c1331de4e45b4f34d30ca322 | Rust | 35,024 | 1,010 | //! cellranger
#![deny(missing_docs)]
use anyhow::{Context, Result, bail, ensure};
use clap::{self, Parser};
use cr_types::cell_annotation::CellAnnotationModel;
use cr_types::sample_def::SampleDef;
use cr_types::types::FileOrBytes;
use cr_types::{LibraryType, TargetingMethod};
use cr_wrap::annotate::AnnotateMro;
use c... |
074eec53b9060d540424cf6804f1d2071c7562249dc2e55aa94d7bee44a90448 | Rust | 35,152 | 941 | //! This captures and analyzes data about barcodes.
#![expect(missing_docs)]
use crate::constants::{CHAIN_TYPES, CHAIN_TYPESX, PRIMER_EXT_LEN};
use crate::reverse_complement;
use io_utils::{fwrite, fwriteln};
use itertools::Itertools;
use metric::{Histogram, JsonReporter, PercentMetric, SimpleHistogram, TxHashMap};
us... |
4bf8f2e6ca86a8e70d2dffed11de4ead52c2c046b3d25cc354b819a3077f7838 | Rust | 35,473 | 1,105 | //! Crate for VarTrix.
//!
//! Computes allele counts given alignment shards and a barcode list.
#![deny(missing_docs)]
use anyhow::{Context, Result, bail};
use barcode::Barcode;
use bio::alignment::Alignment;
use bio::alignment::pairwise::banded::Aligner;
use bio::io::fasta;
use cr_types::{BamContigInfo, BarcodeIndex}... |
d0326844cb762b3e3418bea7716fdb3f65eb52d96b18ba3357fe28142cce3b78 | Rust | 39,971 | 1,003 | //! Martian stage PARSE_MULTI_CONFIG
#![deny(missing_docs)]
use super::setup_reference_info::get_reference_info;
use crate::preflight::hostname;
use crate::{MultiParams, index_schemes_to_custom_chemistry_defs};
use anyhow::{Result, anyhow, bail};
use base64::Engine;
use base64::prelude::BASE64_STANDARD;
use cr_types::... |
e222a56febb7333d1a1f55afbb799a52e399be7be2ff7dc0215464b31352ef02 | Rust | 40,194 | 1,116 | //! Trim adapters from reads using a combination of
//! k-mer matches, sparse alignment and banded alignment.
//! Inspired by the [cutadapt](https://cutadapt.readthedocs.io/) tool.
//!
//! # Features/Limitations
//! * Supports regular, anchored and non-internal, 3' and 5' adapter trimming
//! * Linked adapters are not ... |
aa320977832aa2548bdc3452e4b126b00ec0ad01b542a66f8c63b5968aa4ee04 | Rust | 41,521 | 1,215 | //! The file contains reference-free code for finding paths in a graph and
//! simplifying it.
#![deny(missing_docs)]
#![expect(clippy::many_single_char_names)]
use graph_simple::GraphSimple;
use hyperbase::Hyper;
use std::cmp::max;
use std::iter::zip;
use std::mem::swap;
use vector_utils::{
bin_member, bin_positi... |
3e72a926d35b7e745ee90004e43208afddb31a96f43a8e3e51b07e265271b5ac | Rust | 41,870 | 1,167 | #![deny(missing_docs)]
use crate::aligner::BarcodeSummary;
use anyhow::Result;
use barcode::Barcode;
use cr_types::probe_set::{
MAPQ_GAP_MAPPED_NOT_WITHIN_MAX_ERR, MAPQ_HALF_MAPPED, MAPQ_SPLIT_MAPPED,
};
use cr_types::rna_read::RnaRead;
use cr_types::{GenomeName, LibraryType};
use itertools::Itertools;
use json_re... |
6f227b82342b87994f73ceba0fba9fa87c094b335f13eb8cdffca19e0985670a | Rust | 42,095 | 1,145 | //! Martian stage SUMMARIZE_VDJ_FILTERS
#![expect(missing_docs)]
use crate::matrix::{H5File, gex_umi_counts_per_barcode};
use anyhow::Result;
use cr_lib::parquet_file::{ParquetFile, ParquetWriter, PerBarcodeFilter};
use enclone_process::BarcodeFate;
use itertools::Itertools;
use martian::prelude::*;
use martian_derive... |
d9fb9d40163b8530d214ab7d9d5c29f44a0ccc9e8c0166528cb098584ee31060 | Rust | 42,631 | 1,052 | //! Identifies canonical adapter configurations in long-read sequencing data
//! and uses flanking adapters to extract 10x library constructs.
use crate::WhichRead;
use crate::adapter_trimmer::{Adapter, AdapterTrimmer};
use crate::adapters::AdapterKind;
use crate::read_pair::{
MAX_READ_HEAD, MAX_READ_LEN, MutReadPa... |
2aeaa5d5ac58ff1d0b01ecb7d7117fd46e2d17ad1f404cf06045c549c6ef9478 | Rust | 44,177 | 1,282 | #![expect(missing_docs)]
use anyhow::{Context, Result};
use barcode::whitelist::ReqStrand;
use cr_types::reference::genome_of_chrom::genome_of_chrom;
use cr_types::{AlignerParam, GenomeName, utils};
use fastq_set::WhichEnd;
use martian_filetypes::FileTypeRead;
use martian_filetypes::tabular_file::TsvFileNoHeader;
use m... |
58a77d068ccf2dad5eb911881e4c3d5135bca4832b3ba4ccd63aed627f6b8440 | Rust | 44,205 | 1,400 | #![expect(missing_docs)]
use crate::reference::feature_reference::FeatureReference;
use anyhow::{Context, Result, bail, ensure};
use barcode::{Barcode, BarcodeConstruct, BarcodeFromString, BcSegSeq};
use itertools::Itertools;
use martian::{AsMartianPrimaryType, MartianFileType, MartianPrimaryType};
use martian_derive::... |
e69e9e5949f44850c1b51f463aa9b81165b6988faf4f0dc1a803fd30b8834bdd | Rust | 45,427 | 1,356 | //! Crate for dealing with 10x barcodes.
//!
//! Contains tools for loading barcode whitelists, check barcodes against the whitelist
//! and correcting sequencing errors in barcodes.
#![expect(missing_docs)]
use std::fmt;
use std::iter::{self, FromIterator};
use std::ops::Deref;
use std::str::FromStr;
pub mod binned;... |
3f35f18bee0e0ee0050294672e9558c2f6a262bd5de716858d1ecc48315d40af | Rust | 46,116 | 1,296 | // Copyright (c) 2018 10x Genomics, Inc. All rights reserved.
#![expect(missing_docs)]
//! Container for the FASTQ data from a single sequencing 'cluster',
//! including the primary 'R1' and 'R2' and index 'I1' and 'I2' reads.
use crate::read_pair_iter::RecordCount;
use crate::{ERROR_CODE_INFO, WhichEnd};
use anyhow:... |
e75464c236cdeb1cafea24ec545bbcd8175ff9ac2de76cdaa18884f7f96a2d57 | Rust | 47,756 | 1,246 | //! Create the web summary and metrics.
#![expect(missing_docs)]
#![allow(clippy::wildcard_imports)]
use super::metrics::MetricTier;
use super::websummary_vdj::*;
use crate::alert::AlertLevel;
use crate::{
Alert, AlertContext, AlertSpec, ChartWithHelp, GenericTable, MakePretty, RawChartWithHelp, Tab,
TableRow,... |
c6278093239011e01431a6f669304720998cf85d117f4a84a1e56a9faeb9c686 | Rust | 49,607 | 1,238 | #![expect(missing_docs)]
use super::probe_set_reference::TargetSetFile;
use crate::probe_set::{ProbeSetReferenceMetadata, is_deprecated_probe, strip_deprecated_prefix};
use crate::reference::reference_info::ReferenceInfo;
use crate::{FeatureBarcodeType, FeatureID, FeatureName, GenomeName, LibraryType};
use anyhow::{Con... |
b923f86815003586fc56d014c3e21411c854f2e0432cf604016f11d37ed48692 | Rust | 50,649 | 1,303 | //! Martian stage ALIGN_AND_COUNT
#![deny(missing_docs)]
use super::write_minimap_index::MinimapIndex;
use crate::BcUmiInfoShardFile;
use crate::align_and_count_metrics::StageVisitor;
use crate::align_metrics::{BarcodeMetrics, LibFeatThenBarcodeOrder};
use crate::aligner::{Align, Aligner, AlignmentOptions, BarcodeSumm... |
19fab2ba8722c059487be82ea83d2bb0ab37285a99c9a670ffcf77e58d4635d3 | Rust | 51,430 | 1,332 | // This is code for a rust-only implementation of stage ASSEMBLE_VDJ.
#![expect(missing_docs)]
//
// ◼ The way we generate a bam file here doesn't make sense. In the current
// ◼ implementation, we build sorted bam files, then merge them, which involves
// ◼ interweaving the files. It seems like we could avoid the in... |
83c9d7a085ddd96d6c42d178f58d9b9f7a97bd3fd6f1478c0d819a9a9ff56bf0 | Rust | 52,162 | 1,387 | #![expect(missing_docs)]
use super::{
AntigenSpecificityRow, FunctionalMapRow, Library, MultiConfigCsv, ProbeBarcodeIterationMode,
SampleBarcodeColumn, SampleRow, create_feature_config, multiconst,
};
use crate::cmo_set::load_default_cmo_set;
use crate::config::{ChemistrySet, PROBE_BARCODE_ID_GROUPING, get_def... |
e7fd65e220528293e24cff41ad36b83dd5eafb8c6f464d35e86ebf8a6a073bd6 | Rust | 54,932 | 1,575 | //! This file contains code to make contigs.
#![deny(missing_docs)]
#![expect(clippy::many_single_char_names)]
// TODO: fix these.
#![expect(clippy::needless_range_loop)]
use self::equiv::EquivRel;
use self::graph_simple::GraphSimple;
use self::hyperbase::Hyper;
use self::kmer_lookup::make_kmer_lookup_20_single;
use c... |
e4de03ce619cc33bf60f075ddc7a5b1c22ee04246a7dbb01a6c47a7c33db6d0a | Rust | 56,223 | 1,586 | #![expect(missing_docs)]
use crate::iter::H5Iterator;
use crate::probe_reference_io::ProbeMaybeWithFiltering;
use crate::{
ChunkedWriter, ColumnAction, feature_reference_io, probe_reference_io, scalar_attribute,
};
use anyhow::{Context, Result, bail};
use barcode::{Barcode, BarcodeContent, MAX_BARCODE_LENGTH};
use ... |
d02602b19a02789f2c65d1e00aa53de39ac21d0e69a1d9bca0853d44d0d78cca | Rust | 58,832 | 1,656 | //! This file contains code to process a barcode.
#![expect(missing_docs)]
#![expect(clippy::many_single_char_names)]
use crate::barcode_data::BarcodeData;
use crate::constants::{CHAIN_NONE_POS, CHAIN_TYPES, CHAIN_TYPESX, PRIMER_EXT_LEN};
use crate::contigs::{MakeContigsResult, make_contigs};
use crate::heuristics::He... |
711b13d166014c1e7485a72ae79799f107c97b6d5d9318c0603d8cb7a327d4af | Rust | 60,397 | 1,631 | #![expect(missing_docs)]
use crate::mark_dups::DupInfo;
use crate::transcript::{
AnnotationData, AnnotationParams, AnnotationRegion, PairAnnotationData, TranscriptAnnotator,
};
use anyhow::Result;
use barcode::BcSeq;
use barcode::whitelist::ReqStrand;
use cr_bam::bam_tags::{
ANTISENSE_TAG, EXTRA_FLAGS_TAG, Extr... |
7545c318864d0114c47e9d6ce28ad4387a96550a218882c4c387041e2a011925 | Rust | 61,360 | 1,693 | //! Mappings from symbol sample index set names to sample index sequences
//! for official 10x sample index plate products.
#![expect(missing_docs)]
use lazy_static::lazy_static;
use std::collections::HashMap;
lazy_static! {
pub static ref SAMPLE_INDEX_MAP: HashMap<&'static str, [&'static str; 4]> = {
let... |
89a320990350268d204f101eee1d16b8aba399c58108a26774d53f1fb0f5aea9 | Rust | 65,630 | 1,904 | //! Martian stage PARSE_AGGR_CSV
#![expect(missing_docs)]
use crate::errors::{FieldResolutionErrors, ParseAggrCsvErrors};
use anyhow::{Context, Result, bail};
use cr_types::csv_parser::CsvParser;
use itertools::Itertools;
use martian::prelude::*;
use martian_derive::{MartianStruct, MartianType, make_mro};
use martian_... |
e384504d1dfc09d846a5ba9669a9b7bc546578e79d45ca7b50ab564668d2f573 | Rust | 71,955 | 1,938 | //! ReadPair wrapper object for RNA reads from Single Cell 3' and Single Cell 5' / VDJ ibraries.
//! Provides access to the barcode and allows for dynamic trimming.
#![expect(missing_docs)]
use crate::chemistry::{
BarcodeExtraction, BarcodeReadComponent, ChemistryDef, ChemistryName, UmiReadComponent,
};
use crate::... |
7af3a22e700da3c94b4a411ca37eae7baeb123eda63e62abb83014f55a654c79 | Rust | 78,988 | 2,207 | #![expect(missing_docs)]
use crate::reference::probe_set_reference::{
PROBE_SET_FILE_FORMAT, PROBE_SET_HEADER, TargetSetFile,
};
use crate::reference::reference_info::{MULTI_GENOME_SEPARATOR, ReferenceInfo};
use crate::types::{AlignerParam, GenomeName};
use anyhow::{Context, Result, anyhow, bail, ensure};
use bio:... |
4777e19aa037e64832efc4b170d4f8197c61c6e01b2edfdfdbc5861e5fda02ee | Rust | 84,318 | 2,530 | //! Specification of analysis chemistries.
#![deny(missing_docs)]
pub mod adapter;
mod chemistry_defs;
use crate::LibraryType;
use anyhow::{Result, bail, ensure};
use barcode::whitelist::{BarcodeId, ReqStrand};
use barcode::{BarcodeConstruct, BcSegSeq, Segments, Whitelist, WhitelistSource, WhitelistSpec};
use chemist... |
6bea02dc6d763a3614111e9d76398e005ab0fc162e3d259d859077d6d10f31e2 | Rust | 105,163 | 2,699 | //! Martian stage DETECT_CHEMISTRY
#![deny(missing_docs)]
use crate::barcode_overlap::FRPGemBarcodeOverlapRow;
use crate::detect_chemistry::adapter_filter::preprocess_units;
use crate::detect_chemistry::chemistry_filter::{
ChemistryFilter, DetectChemistryCandidates, DetectChemistryUnit, LoadedUnit, UnitsPerLibrary... |
502d27d0b74b44e754374710c06cb87dfdca58b80ca6e564db1c33c7834e09b7 | Rust | 106,801 | 2,735 | //! Martian stage WRITE_MULTI_WEB_SUMMARY
//! Write HTML files for websummaries.
#![deny(missing_docs)]
use super::parse_multi_config::CellCalling;
use crate::cell_annotation_ws_parameters::{
CellAnnotationMetrics, CellTypeWebSummaryBundleValue, WebSummaryCellTypeInputs,
generate_cell_type_barchart_from_value,... |
b3c9d217f4af6e9881fd31f774febdc79bb0949843d193da0f7ae54948daa878 | Rust | 132,355 | 3,641 | //! This file contains code to annotate a contig, in the sense of finding alignments
//! to VDJ reference contigs. Also to find CDR3 sequences. And some related things.
// Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#![expect(missing_docs)]
use crate::align::affine_align;
use crate::refx::RefData;
use... |
6e52992a803d86188473c685686fd89758f8ee61bd0e466248b90f2547affe7b | Rust | 191,740 | 5,363 | //! Multi config CSV
#![deny(missing_docs)]
pub(super) mod csv;
pub(super) mod parse;
pub mod preflight;
pub(super) mod scsv;
use self::csv::CsvParser;
use self::multiconst::FUNCTIONAL_MAP;
use self::parse::{
Parse, ParseCtx, parse_prefixed_plate_range, parse_prefixed_range, parse_range, parse_vec,
};
use self::p... |
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