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docs: update wiki for v2 CLI interface - Use 'intronIC extract' subcommand instead of '-s' flag for extraction - Note that streaming mode is now the default - Update --streaming to --no-streaming for disabling streaming - Mention '-s' flag still works as alternative
docs: note that streaming mode is now the default in Overview
docs: update Technical-algorithm.md for v2 defaults - Note that streaming mode is now the default - Remove outdated normalizer save/reload advice (pretrained model includes scaler) - Simplify PWM table to compact bullet list format
docs: update language to reflect pretrained model as default - Clarify that classification uses pretrained SVM model by default - Mention custom training as option for specialized use cases - Fix typo: inronIC -> intronIC
docs: update example scatter plot images - Replace scatter plot images with newer versions from run_tests - Rename C. elegans image to include .cds for consistency - Update Overview.md reference to match renamed file
docs: update wiki to reflect streaming mode as default Update documentation to reflect that streaming mode is now the default in v2.0.0. This provides better performance (2-3x faster with parallel processing) and dramatically lower memory usage (73-90% reduction). Changes to Usage-info.md: - Updated performance options to show --in-memory and --streaming flags - Clarified that streaming is the default mode - Updated examples to remove redundant --streaming flags - Added example for --in-memory mode for small genomes Changes to Example-usage.md: - Reorganized "Parallel processing" section to emphasize streaming default - Replaced "Streaming mode" section with "Memory modes" section - Added explicit comparison of streaming (default) vs in-memory (legacy) - Updated examples to show streaming is automatic - Documented performance benefits (2-3x speedup, 85% memory savings) Key messaging: - Streaming mode is now automatic - no flag needed - Use --in-memory only for very small genomes or debugging - Parallel processing scales efficiently with streaming mode 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
docs: remove --train flag from wiki documentation Update wiki to reflect v2.0.0 architecture changes: - Remove --train flag from classify command - Update to show separate train/extract/classify workflow - Add extract subcommand documentation - Update filtering summary format to new table layout - Add parallel streaming examples Files updated: - Example-usage.md: Replace --train examples with `intronIC train` command, add `intronIC extract` section - Usage-info.md: Remove --train argument, remove training parameters section, add extract subcommand, update examples - Data-filtering-notes.md: Update filtering summary to new table format 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
docs: move wiki-specific images to wiki repo - Add images/ directory with three example plot PNGs - Update Overview.md to use relative image paths - Enables managing wiki assets independently from main repo 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
docs: minor clarifications to filtering notes - Use dashed flag style (--no-nc instead of --no_nc) - Clarify boundary correction direction ("3 bp downstream") - Simplify duplicate tag description - Remove redundant rationale paragraph (info already in main text) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
docs: update related resources section - Add "Where the Minor Things Are" database (Larue & Roy 2023) - Update MIDB description with paper reference - Fix U12DB URL (was broken) - Note SpliceRack is no longer available 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
docs: use modern dashed flag style (--n-models) Update --subsample_n to --n-models to match current CLI conventions. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Fix normalization documentation: describe actual RobustScaler(with_centering=True) implementation - Technical-algorithm.md: Replace ASCII pipeline diagram with nested list format - Technical-algorithm.md: Correct Stage 3 description - uses standard robust z-score WITH centering, not zero-anchored scaling - Overview.md: Update normalization description to match - Note: ZeroAnchoredRobustScaler exists in codebase but is deprecated/unused
Comprehensive wiki update: technical details, citations, v2 features - Home.md: Added key features, quick links, proper citation - Overview.md: Added scientific background, classification method summary - Quick-start.md: Updated installation methods, dependencies - Data-filtering-notes.md: Expanded with filtering tables, boundary correction - Output-files.md: Added score interpretation, common operations - Training-data-and-PWMs.md: Updated for JSON format, added citations - Example-usage.md: Reorganized, added cross-species section - Usage-info.md: Added intro linking to examples - About.md: Expanded with citations, related resources - _Sidebar.md: Added Technical details link - NEW Technical-algorithm.md: Complete technical documentation - Pipeline overview diagram - PWM scoring details with equations - Zero-anchored robust scaling explanation - SVM architecture and feature augmentation - Training process description - Memory/performance considerations - Scientific references
docs: update wiki for streaming mode, headers, and v2 features - Add --streaming mode documentation (85% memory reduction) - Add --no-headers option for output files - Document that meta.iic and score_info.iic now include headers by default - Update Usage-info.md with current help output - Add streaming examples to Quick-start and Example-usage - Update Overview advanced features list
Note formatting
master --> main
Add file format samples
Update meta.iic file format description
Spelling and minor syntax
Update with U2-type BPS info
Correct old filenames
Syntax
Clarify language
Add --upgrade note
Add caveat about python vs python3
Fix formatting
Change meta.iic example formatting
Add info
Bold over italics
Merge branch 'master' of github.com:glarue/intronIC.wiki