Sequence Analysis and Modern C++ - The Creation of the SeqAn3 Bioinformatics Library

Preface
Acknowledgements
Contents
Part I Background
	1 Sequence Analysis
	2 The SeqAn Library (Versions 1 and 2)
		2.1 History
		2.2 Design Goals
		2.3 Programming Techniques
			2.3.1 Generic Programming
			2.3.2 Template Subclassing
			2.3.3 Global Function Interfaces
			2.3.4 Metafunctions
		2.4 Discussion
			2.4.1 Performance
			2.4.2 Simplicity
				Non-locality
				Code Complexity and Feature Creep
				Unconstrained Templates
				Documentation
			2.4.3 Generality, Refineability and Extensibility
			2.4.4 Integration
				Source-Code Level Integration
				Project-Level Integration
			2.4.5 Summary
	3 Modern C++
		3.1 Type Deduction
			3.1.1 The auto Specifier
				Excursus: Lambda Expressions
			3.1.2 Class Template Argument Deduction (CTAD)
		3.2 Move Semantics and Perfect Forwarding
			3.2.1 Move Semantics
			3.2.2 Reference Types and Perfect Forwarding
			3.2.3 Out-Parameters and Returning by Value
		3.3 Metaprogramming and Compile-Time Computations
			3.3.1 Metafunctions and Type Traits
			3.3.2 Traits Classes
			3.3.3 Compile-Time Computations
			3.3.4 Conditional Instantiation
			3.3.5 Standard Library Traits
		3.4 C++ Concepts
			3.4.1 Introduction
			3.4.2 Defining Concepts
			3.4.3 Using Concepts
			3.4.4 Concepts-Based Polymorphism
			3.4.5 Standard Library Concepts
		3.5 Code Reuse
			3.5.1 The Curiously Recurring Template Pattern (CRTP)
			3.5.2 Metaclasses
		3.6 C++ Ranges
			3.6.1 Introduction
			3.6.2 Range Traits and Concepts
			3.6.3 The View Concept
			3.6.4 Range Adaptor Objects
			3.6.5 Standard Library Views
		3.7 Customisation Points
			3.7.1 Excursus: Calling Conventions
			3.7.2 Introduction
			3.7.3 ``Niebloids\'\'
			3.7.4 Future Standardisation
		3.8 Concurrency & Parallelism
		3.9 C++ Modules
		3.10 Utility Types
		3.11 Discussion
Part II SeqAn3
	4 The Design of SeqAn3
		4.1 Design Goals
			4.1.1 Performance
			4.1.2 Simplicity
			4.1.3 Integration
			4.1.4 Adaptability
			4.1.5 Compactness
		4.2 Programming Techniques
			4.2.1 Modern C++
			4.2.2 Programming Paradigms
			4.2.3 Polymorphism and Customisation
			4.2.4 Aspects of Object-Orientation
			4.2.5 Ranges and Views
			4.2.6 ``Natural\'\' Function Interfaces
			4.2.7 constexpr if Possible
		4.3 Administrative Aspects
			4.3.1 Header-Only Library
			4.3.2 Licence
			4.3.3 Platform Support
				Compiler
				Operating System
				Machine Architecture
			4.3.4 Stability
				API
				ABI
				Platform
			4.3.5 Availability
			4.3.6 Combining SeqAn2 and SeqAn3
		4.4 Dependencies and Tooling
			4.4.1 Library Dependencies
				The C++20 Standard Library
				The Succinct Data Structure Library
				Cereal (Optional Dependency)
				Lemon (Optional Dependency)
				(De-)Compression Libraries (Optional Dependencies)
			4.4.2 Documentation
			4.4.3 Testing
				Test Metrics
				Implementation
				Execution
				Future
		4.5 Project Management and Social Aspects
	5 Library Structure and Small Modules
		5.1 Library Structure
			5.1.1 Files and Directories
			5.1.2 Modules and Submodules
			5.1.3 Names and Namespaces
		5.2 ``Small\'\' Modules
			5.2.1 Argument Parser
			5.2.2 The Core Module
			5.2.3 The Utility Module
				Operations on Characters
				Excursus: Variadic Templates, Parameter Packs and Folds
				Type Lists
			5.2.4 The STD Module
			5.2.5 The Contrib Module
		5.3 Discussion
			5.3.1 Performance
			5.3.2 Simplicity
			5.3.3 Integration
			5.3.4 Adaptability
			5.3.5 Compactness
	6 The Alphabet Module
		6.1 General Design
			6.1.1 Character and Rank Representation
			6.1.2 Function Objects and Traits
			6.1.3 Concepts
		6.2 User-Defined Alphabets and Adaptations
			6.2.1 User-Defined Alphabets
			6.2.2 Adapting Existing Types as Alphabets
		6.3 The Nucleotide Submodule
			6.3.1 General Design
			6.3.2 Canonical DNA Alphabets
			6.3.3 Canonical RNA Alphabets
			6.3.4 Other Nucleotide Alphabets
		6.4 The Amino Acid Submodule
			6.4.1 General Design
			6.4.2 Amino Acid Alphabets
			6.4.3 Translation
		6.5 Composite Alphabets
			6.5.1 Alphabet Variants
			6.5.2 Alphabet Tuples
			6.5.3 Alphabet ``any\'\' Types
		6.6 The Quality Submodule
			6.6.1 General Design
			6.6.2 Quality Alphabets
			6.6.3 Quality Tuples
		6.7 Discussion
			6.7.1 Performance
			6.7.2 Simplicity
			6.7.3 Integration
			6.7.4 Adaptability
			6.7.5 Compactness
	7 The Range Module
		7.1 General Design
		7.2 Container
			7.2.1 Concepts
			7.2.2 Bit-Compressed Container
			7.2.3 Containers of Containers
			7.2.4 Fixed-Capacity Containers
		7.3 Views
			7.3.1 General Design
			7.3.2 Alphabet-Specific Views
			7.3.3 Some General-Purpose Views
			7.3.4 Implementation Notes
		7.4 Discussion
			7.4.1 Performance
				Container
				Views
			7.4.2 Simplicity
			7.4.3 Integration
			7.4.4 Adaptability
			7.4.5 Compactness
	8 The Input/Output Module
		8.1 The Stream Submodule
		8.2 Serialisation
		8.3 Formatted Files
			8.3.1 Files and Formats
			8.3.2 Records and Fields
		8.4 The Sequence File Submodule
			8.4.1 Input
			8.4.2 Output
			8.4.3 Combined Input and Output
			8.4.4 Asynchronous Input/Output
		8.5 Discussion
			8.5.1 Performance
			8.5.2 Simplicity
			8.5.3 Integration
			8.5.4 Adaptability
			8.5.5 Compactness
	9 The Search Module
		9.1 The FM-Index Submodule
			9.1.1 Unidirectional FM-Index
			9.1.2 Bidirectional FM-Index
		9.2 The k-Mer-Index Submodule
			9.2.1 Shapes in SeqAn3
				Excursus: Strong Types
				Shapes
				Hashing
		9.3 General Algorithm Design
		9.4 The (Search) Algorithm Submodule
			9.4.1 Search Strategies
		9.5 The Configuration Submodule
			9.5.1 Excursus: Aggregate Initialisation and Designated Initialisers
			9.5.2 Search Config Elements
		9.6 Discussion
			9.6.1 Performance
				Search
				k-Mers and Shapes
			9.6.2 Simplicity
				Indexes
				Search
				k-Mers and Shapes
			9.6.3 Integration and Adaptability
			9.6.4 Compactness
	10 The Alignment Module
		10.1 The Aligned Range Submodule
			10.1.1 Concepts and Function Objects
			10.1.2 Gap Decorators
		10.2 The Scoring Submodule
			10.2.1 Alphabet Scoring Schemes
			10.2.2 The Gap (Scoring) Scheme
		10.3 The Pairwise (Alignment) Submodule
			10.3.1 Algorithm Interface
			10.3.2 Alignment Result Type
			10.3.3 Theoretical Background and Implementation Details
		10.4 The Configuration Submodule
		10.5 Discussion
			10.5.1 Performance
			10.5.2 Simplicity
				Using the Gap Decorator
				The Algorithm Interface
			10.5.3 Integration
			10.5.4 Adaptability
			10.5.5 Compactness
Part III Lambda
	11 Lambda: An Application Built with SeqAn
		11.1 Introduction
			11.1.1 Previous Work
			11.1.2 History of LAMBDA
		11.2 Implementation
			11.2.1 Index Creation
			11.2.2 Search
		11.3 Results
			11.3.1 Notable Features
			11.3.2 Performance
				Lambda3\'s Parameter Space
				Speed and Sensitivity Compared to Other Applications
		11.4 Discussion
			11.4.1 From SeqAn2 to SeqAn3
			11.4.2 Algorithmic Choices
Part IV Conclusion and Appendix
	12 Conclusion
Appendix A
	A.1 Notes on Reading This Book
		A.1.1 References and Hyperlinks
			Links to External Resources and Websites
			Cross-References Inside the Book
		A.1.2 How to Read Code Snippets
			Line-Numbering in Code Snippets
			Syntax Highlighting
	A.2 Software and Hardware Details
		A.2.1 Benchmarking Environment
		A.2.2 Helpful Software
	A.3 Copyright
		A.3.1 SeqAn Copyright
	A.4 Longer Code Snippets
	A.5 Detailed Benchmark Results (Local Aligners)
References