James Bonfield
Principal Software Engineer at Wellcome Trust Sanger Institute
Cambridge, England, United Kingdom
Summary
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Rockstar🎓
Top SchoolJames Bonfield is a Principal Software Engineer based in Cambridge with over two decades of C and Linux-focused development experience, primarily in DNA sequencing, assembly, editing and visualization. He is the primary developer of the open-source Gap5 editor and has been a steady contributor to flagship bioinformatics projects like samtools, bcftools and htslib, where he improved performance, threading and CRAM support. Known for pragmatic, efficient C code and a deep interest in data compression, he combines low-level systems expertise with rigorous test and QA practices. His background includes porting cross-platform scientific tools and long-term stewardship of genomics tooling at institutions such as the Wellcome Trust Sanger Institute and the MRC Laboratory of Molecular Biology. A not-obvious strength is his focus on modernizing legacy code—replacing old data structures and hardening multithreading—to keep critical genomics libraries maintainable and high-performing.
16 years of coding experience
11 years of employment as a software developer
Bachelor of Science (BSc), Computer Science, Bachelor of Science (BSc), Computer Science at University of Warwick
Github Skills (17)
algorithms10
variants10
testing10
bash10
c1110
data-structure10
c1710
thread10
performance-optimization10
bioinformatics10
data-structures10
compress9
algorithm9
multithreading9
compression9
Programming languages (14)
Github contributions (5)
samtools/samtools
Apr 2014 - Jan 2023
Tools (written in C using htslib) for manipulating next-generation sequencing data
Role in this project:
Back-end Developer & QA Engineer / Test Automation Engineer
Back-end Developer & QA Engineer / Test Automation EngineerContributions:150 reviews, 314 commits, 298 PRs in 8 years 11 months
Contributions summary:James primarily focused on enhancing the testing infrastructure of the samtools library. Their contributions involved adding and modifying test scripts (regression.sh, test.pl, etc.) to validate the functionality of various tools within the package, such as mpileup and view. They implemented new test cases for features like CRAM file handling, base modification, and reference specification, confirming their understanding of the library's core functionality and testing methodologies. Their work also included fixing bugs and ensuring the robustness of the codebase by addressing issues related to buffer overruns and data handling.
next-generationsequencing-datanext-generation-sequencinggenomicssequencing
samtools/htslib
Jul 2013 - Jan 2023
C library for high-throughput sequencing data formats
Role in this project:Back-end Developer
Back-end DeveloperContributions:224 reviews, 665 commits, 468 PRs in 9 years 8 months
Contributions summary:James contributed significantly to the C library for high-throughput sequencing data formats (htslib), focusing on its CRAM implementation. Their work involved adding CRAM support to the htslib library, integrating code from the samtools io_lib subdirectory, and performing a major overhaul of the CRAM code, including replacing legacy data structures with modern equivalents (e.g., replacing io_lib's HashTable and dstring_t types with khash and kstring). The user fixed a variety of bugs, including issues with multi-threading and memory management within the CRAM library.
c-plus-plusbioinformaticsbamcramsequencing-data
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