Andrew Whitwham
Senior Software Developer at Wellcome Trust Sanger Institute
South Cambridgeshire, England, United Kingdom
Summary
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Rockstar🎓
Top SchoolAndrew Whitwham is a Senior Software Developer with 13 years of professional experience based in South Cambridgeshire, currently contributing at the Wellcome Trust Sanger Institute. He specializes in back-end systems for bioinformatics, with substantive open-source contributions to widely used genomics toolkits such as samtools, htslib, and bcftools—work that ranges from core C algorithm changes to file-format support and cloud storage integration. His contributions include implementing FASTQ indexing in htslib, adding duplicate-marking functionality to samtools, and improving usability and error handling across the bcftools suite, reflecting a mix of maintenance, feature development, and robustness improvements. Known for pragmatic engineering, he combines deep domain knowledge of sequencing data formats with attention to licensing and operational details that keep critical scientific tooling reliable in production.
13 years of coding experience
5 years of employment as a software developer
De Montfort University
Stackoverflow
1reputation
0reached
0answers
0questions
Github Skills (20)
python10
sequence-alignment10
c1110
c1710
bioinformatics10
genomics10
bcftools10
data-structure9
algorithm9
algorithms9
amazon-s39
aws-s39
s3-bucket9
data-structures9
vcf-files8
Programming languages (7)
Github contributions (5)
samtools/samtools
Aug 2017 - Jan 2023
Tools (written in C using htslib) for manipulating next-generation sequencing data
Role in this project:
Back-end Developer
Back-end DeveloperContributions:45 reviews, 101 commits, 175 PRs in 5 years 6 months
Contributions summary:Andrew contributed significantly to the `samtools/samtools` repository, focusing on the addition of new features, such as `markdup` to mark duplicates, and the addition of the `--both-ends` and `--tolerance` features in the ampliconclip sub-command. The work involved modifications to core C code, including changes to data structures and algorithms related to alignment processing. These contributions enhanced the functionality and user experience of the samtools toolkit.
next-generationsequencing-datanext-generation-sequencinggenomicssequencing
samtools/htslib
Mar 2018 - Jan 2023
C library for high-throughput sequencing data formats
Role in this project:Backend Developer
Backend DeveloperContributions:22 reviews, 29 commits, 150 PRs in 4 years 10 months
Contributions summary:Andrew primarily focused on enhancing the `faidx` functionality within the `htslib` library to support FASTQ file indexing. They implemented code to read and index FASTQ files, similar to FASTA, and addressed related bug fixes. Furthermore, the user worked on allowing removed VCF headers to be replaced and added code related to S3 bucket configurations, query strings, and file part sizes within the hfile library. These changes involved both file format handling and cloud storage integration.
c-plus-plusbioinformaticsbamcramsequencing-data
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