SeqAn3 – Sequence Analysis and Modern C++

Abstract

This thesis introduces SeqAn3, a new software library built with Modern C++ to solve problems from the domain of sequence analysis in bioinformatics. It discusses previous versions of the library in detail and explains the importance of highly performing programming languages like C++. Complexity in the design of the library and of the programming language itself are identified as the major obstacles to user satisfaction, widespread adoption and long-term viability of the project. Therefore, based on very fundamental changes in the C++ programming language, a new library design is formulated and implemented. Its impact is showcased by porting the local aligner called Lambda from SeqAn2 to SeqAn3. Both, the library and the application are highly relevant in practice and prove that simpler and more compact solutions are possible. This thesis documents the process of creating said software, contributing vital information to the fields of research software engineering, library design and to a certain degree also applied programming language research. As one of the first larger projects to be designed fully around C++20 features, it has instructive value beyond bioinformatics.