This change introduces the `obiprimers` command-line tool and a complete search pipeline for identifying primer pairs. It includes new data structures for pair evaluation, comprehensive search configuration options, and detailed CSV output handling for results.
Corrects the indexing strategy for seed searching, improving performance and introducing a new seed index structure for efficient pattern lookup.
This commit updates the core matching logic by shifting the indexing strategy to use two halves of k/2 bases, resulting in significant speed improvements for sequence matching. It also introduces a new `seedIndex` structure for fast pattern retrieval and implements comprehensive performance testing logic for matching functions. Future features, such as bit-parallel search, are deferred.
This change introduces the core functionality for identifying, validating, and statistically evaluating primer pairs within the corpus. It includes new data structures for primer parameters, amplicon statistics, and sequence handling, along with methods for assigning taxa to sequences. Comprehensive tests are added to ensure the accuracy of the pair evaluation against expected outputs.
This commit introduces the core matching functionality, including parallel corpus loading, the `Corpus` data structure, and implementations for `matchNaive` and `matchApat`. It also defines new matching rules, variant handling, and comprehensive unit and integration tests to validate the new logic and parameter handling.
This change introduces thread-safe pipe registration and unregistration functions using `sync.WaitGroup` and `atomic.Int64` to manage the count of registered pipes, addressing a race condition identified by the race detector.
This introduces new structures for defining sequence roles and constraints, core logic for strict word identification, and comprehensive unit tests to ensure accuracy and correct behavior.
Introduces the SeqKmerCounter structure for parallel k-mer counting, refactors sequence reading and writing logic, and adds comprehensive test coverage for various sequence scenarios.
Introduces parallel processing for clustering, refines scoring mechanisms, and expands test coverage for the alignment functionality.
This change introduces parallel processing capabilities within the clustering logic, updates the core similarity engine with new data structures and scoring methods, and implements a comprehensive test suite for the alignment tool. It also adds new command-line options for configuring alignment parameters and reference lengths.
This update introduces the core clustering algorithm, including parallel execution, dynamic block sizing, and SIMD-accelerated scoring methods. It also adds robust sequence preparation, k-mer analysis, and comprehensive test data fixtures for validation.
Introduces the BandedLCS function for efficient LCS scoring, supporting both scalar and SIMD implementations. Adds comprehensive unit tests, benchmarking utilities, and error handling for sequence constraints.
The changes introduce new configuration options for clique searching, state tracking for search outcomes, and logic for handling unreachable targets. Tests are added to verify search modes, failure conditions, and the correctness of coloring bounds.
Introduces a mechanism for tracking progress during clique finding operations. This includes implementing a progress bar state management system, handling visibility checks, and integrating progress reporting into the clique finding logic and result processing.
This commit updates the project to use Go version 1.27 for all build and testing processes. It also introduces support for experimental SIMD code compilation, enabling it by default while ensuring a portable scalar fallback is available. Documentation has been updated to reflect the new Go version and the use of the experimental SIMD package.
This commit introduces core functionality for oligonucleotide family tagging, constrained k-mer generation, and clique finding. It also includes updates to the Go language version and refactors the logic for k-mer dissimilarity metrics.
Introduces k-mer distance structures and SIMD implementation for LCS simulation.
Adds support for concurrent, read-only k-mer partners, implements data preparation for SIMD alignment, and adds comprehensive testing and benchmarking capabilities.
Adds support for Hamming distance, constrained k-mer generation, and optimized Longest Common Subsequence (LCS) calculations using scalar, batch, and SIMD methods.
This includes new methods for k-mer distance calculation, structures for k-mer constraints, and SIMD-based batch processing for LCS to improve performance and correctness.
Updates project settings such as the name, activation timeout, and supported languages. Modifies the FilterOn method in the batch iterator to handle sequence filtering and pushing to the iterator.
Corrects expected values for division and comparison operations in the uint128 test suite. Updates obilandmark to use log.Fatalf instead of log.Fatal, ensuring sequence ID, taxid, and taxonomy name are correctly interpolated in fatal error messages.
Introduce explicit input validation and a `(-1, -1, -1)` sentinel return value to signal invalid or unreliable matches. Add pre-call length checks and early returns to prevent panics during indel relocation. Fix an index offset bug in coordinate calculation by preserving the original fragment position before applying alignment deltas. Update match filtering to enforce reliability checks only on successfully relocated alignments. Comprehensive tests validate edge cases, boundary constraints, and error thresholds.
The options system now tracks explicit file paths via a new accessor and functional option. This filename is threaded through the FASTQ parser chain to replace generic source references in fatal error messages, providing clearer, file-specific diagnostics without altering core parsing logic or test suites.
The change replaces numeric threshold checks with an explicit flag state tracker for the `--allowed-mismatches` option. This ensures per-primer mismatch settings from configuration files are preserved when the CLI parameter is omitted or zero, making the command-line flag act strictly as an explicit override rather than a default fallback.
Introduce a streaming JSON parser that decodes biological sequences using `goccy/go-json` with configurable batching to minimize memory overhead. Extend the CLI, file suffix filters, and MIME type detection to automatically recognize and route JSON inputs. Refactor header parsing into a centralized switch-case handler for improved maintainability.
Adds `.gitignore` rules to exclude benchmark outputs and local build artifacts. Initializes Serena AI configuration for the Go project with UTF-8 encoding and gitignore-based file exclusion. Refactors the FASTSEQ header parser to fix regex syntax, optimize alternation ordering, improve control flow readability, and introduce explicit float-to-int coercion that preserves fractional values.
Corrects duplicated typos in the registered GVal function names, changing "which_maxwhichmax" and "which_minwhichmin" to "which_max" and "which_min". The underlying obiutils.WhichMax/WhichMin logic and its int-to-float64 index conversion remain unchanged.
Implement reflection-based WhichMax and WhichMin to dynamically find the index or key of the maximum/minimum element in slices, arrays, or maps. Functions validate orderability, handle empty collections, and dispatch via reflect.Kind. Expose as which_max and which_min GVal functions, with float64 type assertions for compatibility and preserved error handling.
Introduces an `unwrapInterface` reflection helper to dereference `interface{}`-wrapped values before type validation. Updates slice and map iteration loops in min/max functions to apply this helper, ensuring `isOrderedKind` accurately identifies underlying concrete types instead of incorrectly rejecting `reflect.Interface` elements.
Extends OBI header parsing to recognize and deserialize JSON-like arrays and objects. Introduces safe conversion utilities in `obiutils` to cast generic interface values into typed maps, and exposes them via new `BioSequence` methods. Header values are now marshaled, quote-normalized, and formatted for map and slice types.
Multiple raw k-mers collapsing into identical circular canonical forms introduce bias into complexity estimates. This change pre-computes `log(class_size)` tables and per-word-size maximum entropy bounds. The `KmerEntropy` function and `KmerEntropyFilter` are updated to apply the corrected formula `(log(N) + Σf·log(s) - Σf·log(f))/N / emax`, ensuring accurate sequence complexity estimation.
Introduce generic and reflection-based utilities for filtering slices and maps by minimum/maximum thresholds, along with saturating subtraction. The `obiutils` package provides type-safe generic implementations alongside dynamic reflection dispatchers to handle arbitrary ordered and numeric types. These are exposed as GVAL expression functions in `obiseq`, extending the language's built-in filtering and numeric capabilities.
Adds a pre-processing guard that checks for empty sequence identifiers before formatting. This prevents malformed FASTA output and stops downstream processing of invalid FASTQ data by terminating early. The check is placed before existing sequence-length validations to enforce non-empty IDs during batch processing.
- **obiconvert**: Added `--raw-taxid` mode to output numeric taxIDs without formatting (e.g., "12345" instead of ":tax:NCBI_0987@species"). Introduced `TaxNode.FullString()` to reliably return full formatted strings regardless of global settings, and improved fallback behavior when taxonomy DB is unavailable.
- **ngsfilter**: Input fields (primers, sample tags/IDs) are now automatically trimmed of leading/trailing whitespace to prevent parsing failures from inconsistent formatting.
- **obitools (pcrtag)**: Mismatch-related fields (`forward_mismatches`, `reverse_mishaps`) renamed to "error" for consistency across annotation dictionaries.
- **obipairing & obtagpcr**: Enforced mandatory paired-end file input (`--forward` and `reverse`) in obipairing; added CLI support for generating config templates via AskConfigTemplate(); removed redundant `Required()` constraints and introduced helper function CLIHasPairedFiles().
- Add new `--tax-id` mode (`obiconvert --raw-taxid`) to output bare numeric taxIDs instead of full-format strings.
- Introduce `TaxNode.FullString()` to always return the complete "code:id [name]@rank" format, regardless of global `UseRawTaxids()` setting.
- Update `.String(taxonomyCode)` to respect the global flag, returning bare ID when `--raw-taxid` is active.
- Extract raw taxID from full-format strings in taxonomy methods when needed (e.g., fallback without loaded DB).
- Add comprehensive test suite covering:
a) `--raw-taxid` execution and idempotency
b) full-format taxID output with `--taxonomy`
c interaction of both flags
d format validation
- Add test data: new reference files `out_ecotag.fasta`, taxonomy.csv, and updated shell script.
Trim leading/trailing whitespaces in forward/reverse primers, tags (via sample_tag), experiment andsample fields to prevent parsing errors due to formatting inconsistencies in input data.
- Renamed `obimultiplex_forward_mismatches` to "error" for consistency
- Similarly renamed
`obimultiplex_reverse_mismatches` to "error"
- Applied changes in both annotation dictionaries (aanot, banot)
- Enforce requirement of both forward (-F) and reverse files in obipairing/main.go
- Add config template support to obtagpcr via CLIAskConfigTemplate()
- Remove redundant Required() constraints in options.go
- Introduce new helper CLIHasPairedFiles()
- Added strict length matching between sequences and quality scores in `SetQualities`, `Take Qualites` (note: likely intended as " TakeQuantiles" or similar, but preserved per commit), and `Subsequence` operations; an error is now raised if lengths do not match.
- Introduced a new `map_summaries` aggregation feature in obisummary to merge map summary data across datasets, supporting safe concurrent access and inclusion of non-empty results in the final output.
- Centralized string reversal logic via a new `inverser_chaine()` utility function, replacing duplicated inline implementations throughout the codebase.
- Implement merging logic of `map summaries` across datasets
- Ensure proper initialization and population in multi-threaded context
- Add `map_summaries` to final output dictionary when non-empty
Eric Coissac