attractivechaos/klib
Klib
klib is a comprehensive C standard library extension and data structure toolkit. It provides a set of fundamental tools for memory management, data organization, and general-purpose utility functions for standalone C applications.
The project features specialized capabilities for bioinformatics sequence analysis, including the parsing of FASTA, FASTQ, and Newick formats and the implementation of Smith-Waterman sequence alignment and Hidden Markov Models. It also includes a mathematical computation library for numerical routines and expression evaluation, as well as a lightweight HTTP and FTP client for random-access remote data retrieval.
The toolkit covers a broad surface of high-performance computing primitives, including multi-threading models, linear-time suffix array construction, and optimized sorting algorithms. It implements a variety of efficient data indexing structures such as hash tables with open addressing, B-trees, and intrusive AVL trees, supported by memory-pool-based sequence management.
Additional utilities include JSON data parsing and command-line argument interpretation.
Features
- Sequence Analysis - Provides tools for analyzing biological sequences, including FASTA/FASTQ parsing and Smith-Waterman alignment.
- Bioinformatics Sequence Analysis Libraries - Provides a specialized set of tools for parsing biological formats and performing sequence alignment.
- Sequence Alignment - Implements the Smith-Waterman algorithm to perform local sequence alignment for biological data comparison.
- Striped Smith-Waterman Alignment - Performs high-performance local sequence alignment using the Striped Smith-Waterman algorithm for genomic data comparison.
- Bioinformatics Sequence Parsing - Reads and processes specialized biological file formats, including FASTA and FASTQ, for genomic analysis.
- Data Indexing Structures - Organizes information using hash tables, B-trees, and AVL trees for high-performance lookups.
- Key-Value Pair Managers - Provides efficient key-value storage and retrieval using hash tables with open-addressing collision resolution.
- Intrusive AVL Trees - Provides memory-efficient intrusive AVL tree structures for managing sorted hierarchies without additional allocations.
- Tree Data Structures - Provides B-trees and AVL trees to organize data hierarchically for efficient searching and range queries.
- Search Tree Implementations - Implements balanced search trees, including B-trees and intrusive AVL trees, to enable efficient data lookup.
- C Data Structure Libraries - Provides low-level C implementations of fundamental data structures including hash tables, B-trees, and AVL trees.
- C Libraries - Serves as a portable C library extension providing general-purpose data structures and utility functions.
- C Memory Management - Handles low-level allocation and cleanup of memory buffers using custom memory pools and dynamic arrays.
- Pool Allocators - Utilizes pool allocators to manage contiguous memory blocks for linked lists and queues, reducing fragmentation.
- Linked List Implementations - Implements efficient single-linked lists integrated with memory pools for low-level data organization.
- C Runtime Utilities - Supplies a comprehensive suite of C runtime utilities for JSON parsing, CLI argument handling, and math evaluation.
- Dynamic Sequence Management - Organizes data using a combination of dynamic arrays, double-ended queues, and linked lists supported by memory pools.
- C Numerical Libraries - Implements numerical routines, nonlinear programming, and random number generation in C.
- Dynamic Arrays - Implements resizable dynamic arrays that automatically manage contiguous memory blocks for element storage.
- Open Addressing Implementations - Implements hash tables using open addressing and probing techniques for efficient key-value storage.
- Hidden Markov Models - Provides Hidden Markov Model implementations for the analysis of probabilistic biological sequences.
- Mathematical Evaluators - Includes logic to parse and evaluate mathematical formula strings into numerical results.
- Newick Format Parsing - Converts Newick tree format text into structured data for biological and hierarchical analysis.
- Collection Sorting - Implements high-performance collection sorting using a hybrid introsort algorithm to ensure linearithmic time complexity.
- Remote File Reading - Enables reading specific byte ranges from remote HTTP or FTP servers using random access.
- Random Access Remote Retrieval - Provides a lightweight client for random-access retrieval of specific data segments from HTTP and FTP servers.
- Remote Data Retrieval Libraries - Implements a lightweight client for random-access data retrieval from HTTP and FTP servers.
- Concurrent Thread Execution - Implements multi-threading models to enable parallel task processing and increase overall throughput.
- High-Performance Computing - Implements multi-threading models and optimized sorting algorithms to increase processing speed for large datasets.
- Numerical Computation Routines - Executes numerical routines including nonlinear programming and pseudorandom number generation.
- Recursive Descent Evaluators - Implements a recursive-descent evaluator to parse and compute results from mathematical formula strings.
- Suffix Array Construction - Implements the SAIS algorithm for linear-time construction of suffix arrays used in string indexing.
- Build Systems - A small, lightweight implementation of common algorithms.
- General Utilities - Lightweight implementations of common algorithms and structures.
Star history
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