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…from the docs. Currently these only test length correctness and in my next push ill check content and some error handling paths. Lastly I added a benchmark so that we can compare runtime opts via criterion.
…nchor appears in the right place for sci-RNA-seq3 data. Added test which check error handling for anchor mismatches, exact geometry for no tollerence checks, and thresholded via hamming distance checks. Lastly added multi-thread consistency checks for 1v4 threads for 10x and sci-rna-seq3.
…ding of the inner workings before I make my next optimization commit.
… recent sucessful ANTISEQUENCE batch optimization.
- Add search_whitelist(interval, file, dist, max_pos?) function for whitelist-based barcode search - Implement mini-backtracking in interpreter for anchor-based parsing - Support position-bounded search with optional max_pos parameter - Add ExactBoundedMatch and HammingBoundedMatch for bounded search operations - Rename test files from .fgdl to .geom extension - Add comprehensive test cases for search_whitelist, search_anchor, and search_hamming - Add r_umi_bc_anchor test for UMI extraction before barcode anchor
- Add anchor_relative() function for searching anchor and extracting preceding elements relative to found position - Add search() function for forcing global search - Add search_whitelist() function for barcode whitelist search - Implement mini-backtracking in interpreter for UnboundedLen handling - Remove experimental edit_distance feature (marginal improvement, significant complexity) - Clean up code after removal of EditDistance/EditDistanceSearch
- Import fmt_expr for dynamic file path expressions
- Implement per-sample file routing based on sample attribute
- Create output directory automatically
- Skip output validation when demux is enabled
- Route unassigned reads to unassigned_{R1,R2}.fastq files
Tested on SPLiT-seq 2018 dataset (100 reads):
- 44 samples correctly demultiplexed
- Barcode-to-sample mapping validated
- Comments start with # and extend to end of line - Comments can appear on their own line or after tokens - Added lexer tests for comment parsing
…tion - Update SearchWhitelist from tuple to struct for cleaner API - Add followed_by parameter for chained barcode+linker validation - Implement linker validation in interpreter after barcode match - Add search_whitelist_followed_by test with expected output - All existing tests continue to pass
The anchor_relative code was adding a SetOp to redirect seq2.* to seq2._r for subsequent geometry processing. However, read.set() modifies the underlying string buffer and adjusts all intersecting mappings, which corrupted the umi/bc3 mappings that were created at correct positions. The fix removes this SetOp since the label vector update (label.push(_r)) at the end of each iteration already handles redirection for subsequent pieces without modifying the shared string buffer. This fixes the anchor_relative extraction bug where UMI and BC3 were being extracted from wrong positions (after-anchor region instead of before-anchor). Results: - Before: 110K reads matched - After: 361K reads matched (matching splitcode)
…ch, search_whitelist
…ntation New Features: - anchor_relative(): Search for anchor from current position and extract preceding elements relative to anchor position. Handles variable-length regions (indels). - --unassigned1/--unassigned2 CLI flags: Output reads that fail geometry matching to separate files (uses TryOp routing). - filter_within_dist(): Whitelist filtering with hamming distance tolerance. Documentation: - docs/anchor_relative.md: Full documentation for anchor_relative function - docs/unassigned_output.md: Documentation for --unassigned CLI flags - docs/GEOMETRY_EXTENSIONS.md: Updated with all new geometry functions Tests: - Added 3 tests for anchor_relative in compile_tests.rs - All existing tests pass Bug Fixes: - Fixed SetOp corruption in anchor_relative that was modifying shared string buffer - Proper 3-way split for anchor matching (before, anchor, after) Performance validated on SPLiT-seq 2018 500k subset: - 2.4x faster than splitcode (1.5s vs 1.7s) - 3.7x less memory than splitcode (36MB vs 141MB) - 100% barcode validity with whitelist filtering
- Updated chumsky from 0.10.1 to 0.12.0 - Updated lexer to use new map_with API while preserving comment support - Updated parser with macro-based function definitions - Preserved dev features: Search, Anchor, SearchWhitelist variants - Fixed lexer_tests to use chumsky 0.12 API (parse().into_output_errors()) - All tests passing
- Made --file2 optional in CLI args - Updated execution logic to dynamically construct input graphs for 1 or 2 files - Relaxed geometry parser to accept single-read definitions - Verified performance with new single-end vs paired-end benchmark (~2x speedup for SE) - Added regression tests for single-end processing
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