Marshall's Algorithms and Data Structures Library

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Table of Contents

1. Description

2. System Requirements

3. Building, Installing, and Generating Documentation

4. Available Features

5. Credits

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Description

This is a library I've created which is suitable to housing and testing various algorithms or data structures which I have found missing or lacking amongst the current breadth of C++ libraries. My focus is on bioinformatics related works, but I have taken some pains to make them general.

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System Requirements

Building Requirements: gcc-libs, g++, libc, git, make, bison >= 3.0.4, flex

Use Requirements: libc

Documentation Requirements: Doxygen

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Building and Installing

Build:

$ make

Debug:

$ make debug
$ ./test/test.out

Install:

# make install

Generate Documentation:

$cd doc/
$doxygen Doxyfile

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Available Features

Algorithms:

• Pearson Correlation Matrix generation
• Kendall Correlation Matrix generation
• Spearman Correlation Matrix generation
• Simple Semi-Automated Thread dispatcher using pthreads
• Various statistical functions
• Quick-Merge Sort
• GEO's .soft file format general parser

Datastructures:

• Upper Diagonal Square Matrix template, memory optimized
• Undirected Graph, Vertex, and Edge templates
• bitpacked array, and sparse bitpacked array
• universal GEO .soft file format container

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Credits

Primary Author: Josh Marshall ([email protected])
Conributors: Victor Claremboux