agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/docs/PSEUDOCODE.md

@@ -1,354 +0,0 @@
-# CRISPR-Cas13 Pipeline Pseudocode Specification
-
-**SPARC Phase 2: Pseudocode Design**
-**Project:** CRISPR-Cas13 Bioinformatics Pipeline
-**Date:** 2025-10-12
-**Version:** 1.0
-
-## Table of Contents
-
-1. [Overview](#overview)
-2. [Algorithm Design Principles](#algorithm-design-principles)
-3. [Module Pseudocode](#module-pseudocode)
-   - [Read Alignment Module](#read-alignment-module)
-   - [Off-Target Prediction Module](#off-target-prediction-module)
-   - [Differential Expression Analysis Module](#differential-expression-analysis-module)
-   - [Reporting Engine](#reporting-engine)
-4. [Complexity Analysis](#complexity-analysis)
-5. [Error Handling Strategy](#error-handling-strategy)
-6. [Performance Characteristics](#performance-characteristics)
-
----
-
-## Overview
-
-This document provides comprehensive pseudocode for the CRISPR-Cas13 bioinformatics pipeline, following SPARC methodology standards. Each module is designed with:
-
-- **Language-agnostic** algorithmic descriptions
-- **Clear logic flow** with explicit control structures
-- **Comprehensive error handling**
-- **Performance optimization** considerations
-- **Modular design** for maintainability
-
-### System Architecture Context
-
-```
-Input Data → Alignment Engine → Off-Target Predictor → Immune Analyzer → Reporting Engine
-               ↓                      ↓                      ↓                 ↓
-           BAM Files         Off-Target Scores      DEG Analysis       Visualizations
-```
-
----
-
-## Algorithm Design Principles
-
-### 1. Data Flow Strategy
-- **Streaming Processing**: Handle large genomic datasets without memory overflow
-- **Parallel Execution**: Leverage multi-threading for independent operations
-- **Caching Strategy**: Store frequently accessed reference data in memory
-
-### 2. Optimization Priorities
-1. **Correctness**: Biological accuracy first
-2. **Performance**: Sub-linear complexity where possible
-3. **Scalability**: Handle datasets from 10GB to 1TB
-4. **Fault Tolerance**: Graceful degradation and recovery
-
-### 3. Design Patterns
-- **Strategy Pattern**: Pluggable alignment algorithms (BWT, k-mer, exact match)
-- **Pipeline Pattern**: Sequential data transformation stages
-- **Observer Pattern**: Progress monitoring and metrics collection
-- **Factory Pattern**: Dynamic model instantiation for ML components
-
----
-
-## Module Pseudocode
-
-### Read Alignment Module
-
-**Purpose**: Align RNA-seq reads to reference genome using hybrid BWT and Smith-Waterman approach.
-
-**Algorithm Overview**:
-1. Build BWT index from reference genome (preprocessing)
-2. Perform seed-and-extend alignment using BWT for candidate regions
-3. Apply Smith-Waterman for precise local alignment
-4. Calculate alignment quality scores with MAPQ
-
-**See detailed pseudocode**: [`algorithms/alignment-module.md`](algorithms/alignment-module.md)
-
-**Complexity**:
-- **Time**: O(n × m) for Smith-Waterman, O(n log m) for BWT seeding
-- **Space**: O(m) where m = reference genome size
-
----
-
-### Off-Target Prediction Module
-
-**Purpose**: Predict and score potential off-target sites using machine learning with gradient boosting.
-
-**Algorithm Overview**:
-1. Extract candidate off-target sites using k-mer matching
-2. Compute feature vectors (mismatch patterns, PAM proximity, chromatin state)
-3. Train gradient boosting classifier on labeled off-target dataset
-4. Predict off-target scores with confidence intervals
-5. Rank sites by biological significance
-
-**See detailed pseudocode**: [`algorithms/offtarget-module.md`](algorithms/offtarget-module.md)
-
-**Complexity**:
-- **Time**: O(k × log n) for gradient boosting prediction
-- **Space**: O(k × d) where k = candidates, d = feature dimensions
-
----
-
-### Differential Expression Analysis Module
-
-**Purpose**: Identify differentially expressed genes using DESeq2-style normalization and statistical testing.
-
-**Algorithm Overview**:
-1. Normalize read counts using size factor estimation
-2. Model count data with negative binomial distribution
-3. Perform Wald test for statistical significance
-4. Adjust p-values for multiple testing (Benjamini-Hochberg)
-5. Conduct immune pathway enrichment analysis
-
-**See detailed pseudocode**: [`algorithms/expression-module.md`](algorithms/expression-module.md)
-
-**Complexity**:
-- **Time**: O(g × s × i) where g = genes, s = samples, i = iterations
-- **Space**: O(g × s) for count matrix
-
----
-
-### Reporting Engine
-
-**Purpose**: Aggregate results and generate comprehensive visualizations and reports.
-
-**Algorithm Overview**:
-1. Collect results from all pipeline modules
-2. Generate statistical summaries and quality metrics
-3. Create visualizations (volcano plots, heatmaps, genome browser tracks)
-4. Render HTML/PDF reports with interactive elements
-5. Export data in standard formats (VCF, BED, CSV)
-
-**See detailed pseudocode**: [`algorithms/reporting-module.md`](algorithms/reporting-module.md)
-
-**Complexity**:
-- **Time**: O(n × p) where n = data points, p = plot complexity
-- **Space**: O(n) for data storage
-
----
-
-## Complexity Analysis
-
-### Overall Pipeline Complexity
-
-| Module | Time Complexity | Space Complexity | Parallelizable |
-|--------|----------------|------------------|----------------|
-| Alignment Engine | O(n × m) | O(m + n) | Yes (per read) |
-| Off-Target Predictor | O(k × log k) | O(k × d) | Yes (per gRNA) |
-| Expression Analyzer | O(g × s × i) | O(g × s) | Yes (per gene) |
-| Reporting Engine | O(n × p) | O(n) | Yes (per plot) |
-
-**Where**:
-- n = number of reads
-- m = reference genome size
-- k = number of candidate off-targets
-- d = feature vector dimension
-- g = number of genes
-- s = number of samples
-- i = iteration count
-- p = plot complexity factor
-
-### Bottleneck Analysis
-
-**Critical Path**: Alignment Engine (60-70% of total runtime)
-
-**Optimization Strategies**:
-1. **BWT Indexing**: Precompute and cache reference index
-2. **Parallel Processing**: Distribute read batches across CPU cores
-3. **GPU Acceleration**: Offload Smith-Waterman to GPU for large datasets
-4. **Adaptive Algorithms**: Use exact match for high-identity reads, SW for complex regions
-
----
-
-## Error Handling Strategy
-
-### 1. Input Validation Errors
-
-```
-FUNCTION: ValidateInput
-INPUT: rawData, schemaDefinition
-OUTPUT: validatedData or error
-
-BEGIN
-    IF rawData is null OR empty THEN
-        RETURN error("INPUT_ERROR", "Empty input data")
-    END IF
-
-    FOR EACH field IN schemaDefinition DO
-        IF NOT ValidateField(rawData[field], field.constraints) THEN
-            RETURN error("VALIDATION_ERROR",
-                "Field {field.name} failed constraint {field.constraints}")
-        END IF
-    END FOR
-
-    RETURN validatedData
-END
-```
-
-### 2. Runtime Errors
-
-**Strategy**: Graceful degradation with retry logic
-
-```
-FUNCTION: ExecuteWithRetry
-INPUT: operation, maxRetries, backoffMs
-OUTPUT: result or error
-
-BEGIN
-    retryCount ← 0
-
-    WHILE retryCount < maxRetries DO
-        TRY
-            result ← operation.execute()
-            RETURN result
-        CATCH error AS e DO
-            IF e.type == TRANSIENT_ERROR THEN
-                retryCount ← retryCount + 1
-                Sleep(backoffMs × 2^retryCount)
-            ELSE
-                RETURN error("FATAL_ERROR", e.message)
-            END IF
-        END TRY
-    END WHILE
-
-    RETURN error("MAX_RETRIES_EXCEEDED",
-        "Operation failed after {maxRetries} attempts")
-END
-```
-
-### 3. Resource Exhaustion
-
-**Memory Management**:
-```
-FUNCTION: ProcessLargeFile
-INPUT: filePath, chunkSizeMB
-OUTPUT: processedResults
-
-BEGIN
-    totalMemoryMB ← GetAvailableMemory()
-
-    IF fileSize > totalMemoryMB × 0.8 THEN
-        // Use streaming approach
-        RETURN ProcessFileStreaming(filePath, chunkSizeMB)
-    ELSE
-        // Load entire file
-        RETURN ProcessFileInMemory(filePath)
-    END IF
-END
-```
-
-### 4. Error Classification
-
-| Error Type | Severity | Action | Retry |
-|-----------|----------|--------|-------|
-| INPUT_VALIDATION | High | Reject request | No |
-| ALIGNMENT_FAILURE | Medium | Skip read, log | No |
-| MODEL_LOAD_ERROR | High | Fail pipeline | Yes |
-| NETWORK_TIMEOUT | Low | Retry with backoff | Yes |
-| OUT_OF_MEMORY | High | Switch to streaming | No |
-| CORRUPTED_DATA | Medium | Skip chunk, log | No |
-
----
-
-## Performance Characteristics
-
-### 1. Throughput Targets
-
-**Dataset Size vs. Processing Time**:
-
-| Dataset Size | Expected Runtime | CPU Cores | Memory (GB) |
-|--------------|-----------------|-----------|-------------|
-| 10 GB (small) | 30-45 minutes | 8 | 32 |
-| 100 GB (medium) | 4-6 hours | 32 | 128 |
-| 1 TB (large) | 24-36 hours | 64 | 512 |
-
-### 2. Scalability Characteristics
-
-**Horizontal Scaling**:
-- **Alignment Module**: Near-linear scaling up to 64 cores
-- **Off-Target Predictor**: Linear scaling with number of gRNAs
-- **Expression Analyzer**: Scales with number of samples
-
-**Vertical Scaling**:
-- **Memory**: Required memory = 5-8× raw data size (uncompressed)
-- **Storage**: Intermediate files = 3-4× input size
-- **GPU**: 10-20× speedup for alignment on NVIDIA A100
-
-### 3. Optimization Opportunities
-
-**Algorithmic**:
-1. Replace Smith-Waterman with banded alignment for high-identity sequences
-2. Use approximate nearest neighbor search (HNSW) for off-target candidate selection
-3. Implement incremental PCA for dimensionality reduction in expression analysis
-
-**Infrastructure**:
-1. Distribute alignment across Kubernetes cluster
-2. Cache reference genome index in shared memory (Redis/Memcached)
-3. Use columnar storage (Parquet) for intermediate count matrices
-4. Implement progressive rendering for large visualizations
-
----
-
-## Implementation Notes
-
-### Language-Specific Considerations
-
-**Rust Implementation** (Primary):
-- Use Rayon for parallel iterators
-- Leverage zero-cost abstractions for performance
-- Implement custom memory allocators for large buffers
-
-**Python Bindings** (ML components):
-- Use PyO3 for Rust-Python interop
-- Leverage NumPy/SciPy for matrix operations
-- Use scikit-learn for gradient boosting
-
-### Testing Strategy
-
-**Unit Tests**:
-- Test each algorithm subroutine independently
-- Use property-based testing (QuickCheck) for alignment correctness
-- Mock external dependencies (file I/O, network)
-
-**Integration Tests**:
-- End-to-end pipeline on small synthetic datasets
-- Verify output formats match specifications
-- Performance regression testing
-
-**Validation**:
-- Compare against gold-standard tools (STAR, HISAT2, DESeq2)
-- Validate biological accuracy on benchmark datasets
-- Cross-validate ML models with held-out data
-
----
-
-## References
-
-1. **Burrows-Wheeler Transform**: Burrows, M., & Wheeler, D. J. (1994)
-2. **Smith-Waterman Algorithm**: Smith, T. F., & Waterman, M. S. (1981)
-3. **DESeq2 Methodology**: Love, M. I., et al. (2014)
-4. **Gradient Boosting**: Friedman, J. H. (2001)
-5. **CRISPR Off-Target Prediction**: Haeussler, M., et al. (2016)
-
----
-
-## Version History
-
-| Version | Date | Changes |
-|---------|------|---------|
-| 1.0 | 2025-10-12 | Initial pseudocode specification |
-
----
-
-**Next Steps**: Proceed to SPARC Phase 3 (Architecture) for detailed system design.