Peter Cock
Staff Software Engineer at Affinda
Tasmania, Australia
Summary
🤩
Rockstar🎓
Top SchoolPeter Cock is a Staff Software Engineer based in Tasmania with 21 years of experience building robust backend systems and tooling across bioinformatics, documentation tooling, and packaging ecosystems. He currently leads engineering efforts at Affinda after senior and lead roles in multiple software companies, bringing deep practical experience in CI/build automation, package management, and backend integrations. An active open-source contributor, Peter has improved core tools like samtools and bcbio-nextgen—fixing tricky CIGAR-string handling and hardening pipeline utilities for reproducible variant and RNA-seq analysis. He also improves developer experience through documentation and tooling contributions to projects such as flake8, Sphinx, and Bioconda, showing a rare mix of systems-level C work and meticulous documentation skills. Colleagues rely on him to untangle complex data-processing bugs and to adapt legacy bioinformatics tools for modern packaging and reproducible workflows. Based in Australia, he combines long-term hands-on engineering with a pragmatic focus on reliability and reproducibility in scientific software.
21 years of coding experience
16 years of employment as a software developer
Bachelor of Computing, Bachelor of Computing at University of TasmaniaMarist Regional College
Stackoverflow
1,615reputation
91kreached
58answers
3questions
Github Skills (49)
restructuredtext10
python10
package-management10
scripting10
sphinx10
r10
conda10
rs10
flake10
bash10
c-programming10
script10
file-handling10
linter10
bioinformatics10
Programming languages (37)
Github contributions (5)
samtools/samtools
Mar 2012 - Jul 2015
Tools (written in C using htslib) for manipulating next-generation sequencing data
Role in this project:
Back-end Developer
Back-end DeveloperContributions:53 commits, 3 PRs, 16 comments in 3 years 4 months
Contributions summary:Peter primarily contributed to the "depad" functionality within the `samtools` project, focusing on processing and manipulating CIGAR strings and reference sequences within BAM files. Their work involved fixing bugs related to CIGAR operations, including handling various CIGAR types such as 'D', 'P', 'X', and '=', while also addressing reference sequence handling. Furthermore, they implemented features to integrate and validate against FASTA reference files, improving the accuracy and robustness of the depad tool.
next-generationsequencing-datanext-generation-sequencinggenomicssequencing
chapmanb/bcbb
Dec 2008 - Jun 2021
Incubator for useful bioinformatics code, primarily in Python and R
Role in this project:Backend Developer & Data Scientist
Backend Developer & Data ScientistContributions:30 commits, 1 PR, 2 comments in 12 years 7 months
Contributions summary:Peter finalized the mapping of BioSQL to ontologies and rearranged files for better organization, indicating a focus on data structure and organization. They developed a REST-like API interface to access Ensembl and FlyBase data, demonstrating backend development skills. The user also added parsing for database references and functional descriptions, likely contributing to data integration and analysis within the bioinformatics domain.
pythonpython-bindingsgenomicsr-and-pythonbioinformatics
Find and Hire Top DevelopersWe’ve analyzed the programming source code of over 60 million software developers on GitHub and scored them by 50,000 skills. Sign-up on Prog,AI to search for software developers.