hartwigmedical/hmftools
Nov 2024 – Oct 2025
12 Months active
Languages Used
JavaKotlinRTextC++Python
Technical Skills
BAM processingBioinformaticsCode RefactoringData AnalysisGenomicsJava
Matthew Cooper
PROFILE
Matthew Cooper
Matthew Cooper developed and maintained core genomic data processing tools in the hartwigmedical/hmftools repository, focusing on high-throughput analysis and robust feature delivery. He engineered modules for read deduplication, consensus building, and HLA typing, applying advanced algorithm design and optimization in Java and Python. His work included performance profiling, memory management, and data structure enhancements to accelerate workflows and improve accuracy. By refactoring code for maintainability and implementing rigorous test automation, Matthew ensured reliable, scalable pipelines for clinical genomics. His contributions addressed complex edge cases in BAM/FASTQ processing, variant filtering, and multi-run data merging, demonstrating depth in bioinformatics engineering.
Overall Statistics
Feature vs Bugs
71%Features
Repository Contributions
146Total
Bugs
26
Commits
146
Features
64
Lines of code
32,219
Activity Months12
Your Network
56 people
Work History
October 2025
10 Commits • 2 Features
Oct 1, 2025October 2025 performance summary for hartwigmedical/hmftools. Focused on stability, maintainability, and multi-run data processing to deliver reliable batch analyses and reduce long-term technical debt.
10 Commits • 2 Features
Oct 1, 2025October 2025 performance summary for hartwigmedical/hmftools. Focused on stability, maintainability, and multi-run data processing to deliver reliable batch analyses and reduce long-term technical debt.
October 2025
September 2025
3 Commits • 2 Features
Sep 1, 2025September 2025 monthly summary for hartwigmedical/hmftools focused on delivering robust HLA typing enhancements in the Lilac tool and targeted code-quality improvements. Key outcomes include grouped handling of HLA-DRB3/DRB4/DRB5 and exon-restricted DRB1 analysis, which improved accuracy and completeness in cohort frequency calculations and sequence analysis. Supporting work included lint cleanup to improve maintainability without altering core functionality.
September 2025
3 Commits • 2 Features
Sep 1, 2025September 2025 monthly summary for hartwigmedical/hmftools focused on delivering robust HLA typing enhancements in the Lilac tool and targeted code-quality improvements. Key outcomes include grouped handling of HLA-DRB3/DRB4/DRB5 and exon-restricted DRB1 analysis, which improved accuracy and completeness in cohort frequency calculations and sequence analysis. Supporting work included lint cleanup to improve maintainability without altering core functionality.
August 2025
11 Commits • 3 Features
Aug 1, 20252025-08 monthly summary for hartwigmedical/hmftools: Delivered maintainability improvements, extended genetic analysis capabilities, and hardened data processing workflows. These efforts reduce technical debt, lower production risk, and enable broader, more accurate analyses in downstream pipelines.
11 Commits • 3 Features
Aug 1, 20252025-08 monthly summary for hartwigmedical/hmftools: Delivered maintainability improvements, extended genetic analysis capabilities, and hardened data processing workflows. These efforts reduce technical debt, lower production risk, and enable broader, more accurate analyses in downstream pipelines.
August 2025
July 2025
31 Commits • 17 Features
Jul 1, 2025Monthly performance summary for 2025-07 for hartwigmedical/hmftools. The Lilac module advanced key features and reliability, delivering targeted quality improvements and better scoring fidelity, while maintaining strong code hygiene and observability. Major feature work includes per-gene quality filtering rules with a zygosity penalty, VAF-based filtering, and final score calculation based on total coverage. Structural improvements include hardening SequenceCount creation by fragment restrictions and introducing a Gene class to replace hard-coded strings, enabling easier future refactoring. In parallel, quality and performance refinements across the codebase (lint cleanups, StackSampler enhancements, improved logging, and unit tests for low-depth filtering) improve stability, traceability, and performance. These changes collectively raise scoring accuracy, reduce risk of false positives, and improve maintainability for faster, safer releases.
July 2025
31 Commits • 17 Features
Jul 1, 2025Monthly performance summary for 2025-07 for hartwigmedical/hmftools. The Lilac module advanced key features and reliability, delivering targeted quality improvements and better scoring fidelity, while maintaining strong code hygiene and observability. Major feature work includes per-gene quality filtering rules with a zygosity penalty, VAF-based filtering, and final score calculation based on total coverage. Structural improvements include hardening SequenceCount creation by fragment restrictions and introducing a Gene class to replace hard-coded strings, enabling easier future refactoring. In parallel, quality and performance refinements across the codebase (lint cleanups, StackSampler enhancements, improved logging, and unit tests for low-depth filtering) improve stability, traceability, and performance. These changes collectively raise scoring accuracy, reduce risk of false positives, and improve maintainability for faster, safer releases.
June 2025
8 Commits • 5 Features
Jun 1, 2025June 2025 monthly summary for hartwigmedical/hmftools focusing on delivering core data-model upgrades, robustness improvements, and diagnostics enhancements that translate to faster analyses, higher accuracy, and cleaner repos. Key features delivered include a Lilac Fragment Data Model Overhaul with map-based storage and AminoAcid/Nucleotide records, robust UMI handling with null-safety and data-class improvements, VAF-based variant filtering for improved accuracy, and performance instrumentation enhancements to surface stack samples and refine thread filtering. A repository hygiene update further reduces noise in diffs by excluding generated files from version control. Overall, these efforts increased processing speed, reduced runtime risks, and strengthened measurement capabilities for data-driven decision making.
8 Commits • 5 Features
Jun 1, 2025June 2025 monthly summary for hartwigmedical/hmftools focusing on delivering core data-model upgrades, robustness improvements, and diagnostics enhancements that translate to faster analyses, higher accuracy, and cleaner repos. Key features delivered include a Lilac Fragment Data Model Overhaul with map-based storage and AminoAcid/Nucleotide records, robust UMI handling with null-safety and data-class improvements, VAF-based variant filtering for improved accuracy, and performance instrumentation enhancements to surface stack samples and refine thread filtering. A repository hygiene update further reduces noise in diffs by excluding generated files from version control. Overall, these efforts increased processing speed, reduced runtime risks, and strengthened measurement capabilities for data-driven decision making.
June 2025
May 2025
17 Commits • 2 Features
May 1, 2025May 2025 performance-focused month for hmftools. Delivered a suite of profiling and data-processing optimizations that enable proactive diagnostics, faster reads grouping, and more robust tests. This work directly increases production observability, reduces latency in data processing, and improves reliability of duplicate grouping and fragment handling.
May 2025
17 Commits • 2 Features
May 1, 2025May 2025 performance-focused month for hmftools. Delivered a suite of profiling and data-processing optimizations that enable proactive diagnostics, faster reads grouping, and more robust tests. This work directly increases production observability, reduces latency in data processing, and improves reliability of duplicate grouping and fragment handling.
April 2025
4 Commits
Apr 1, 2025April 2025: Focused on core processing correctness and stability in hmftools. Delivered two critical bug fixes in the Redux reads processing and UMI handling, with targeted commits and added tests to prevent regressions. Overall impact includes improved consensus read accuracy, better handling of unmapped reads, and consistent read naming across UMI collapsing, enabling more reliable downstream analyses. Technologies demonstrated include flag-driven processing logic, test-driven development, and robust git traceability.
4 Commits
Apr 1, 2025April 2025: Focused on core processing correctness and stability in hmftools. Delivered two critical bug fixes in the Redux reads processing and UMI handling, with targeted commits and added tests to prevent regressions. Overall impact includes improved consensus read accuracy, better handling of unmapped reads, and consistent read naming across UMI collapsing, enabling more reliable downstream analyses. Technologies demonstrated include flag-driven processing logic, test-driven development, and robust git traceability.
April 2025
March 2025
8 Commits • 2 Features
Mar 1, 2025March 2025 focused on increasing accuracy and performance of read deduplication in hmftools, along with strengthening test automation and pipeline reliability. Key deliverables span three areas: (1) Illumina UMI collapsing improvements including PolyG tail handling, jitter-aware grouping, caching of original coordinates, and a PolyG tail requirement of at least two Gs, with integration of pre-collapsed coordinates in BamWriter; expanded tests accompanied by targeted edge-case scenarios. Representative commits include c6ea97ed28a37f18f70ba8168ad527d41aedec3d, 4ff71f75274dea7882666c70e18986269143f28e, 31beee0b728424c9d46da567586aef834e88df41, a6915199bc24924877f6b711d54904ff2d0605ec, de1e4a2c9638d2d12f7036e81340f8a2169ce188, cca4b3a047e01188a7f1fbc192b8da0dd4974d1c; (2) PartitionReader fix: only check MATE_CIGAR_ATTRIBUTE when the mate is mapped, preventing errors in paired-read processing (ac5b4976b2048ecd19c0b4450915825602775c10); (3) Redux module upgrade to JUnit 5 with TestGenerator for improved test generation and coverage (7abeea6a8089b1249629174bfc3500f23696be68).
March 2025
8 Commits • 2 Features
Mar 1, 2025March 2025 focused on increasing accuracy and performance of read deduplication in hmftools, along with strengthening test automation and pipeline reliability. Key deliverables span three areas: (1) Illumina UMI collapsing improvements including PolyG tail handling, jitter-aware grouping, caching of original coordinates, and a PolyG tail requirement of at least two Gs, with integration of pre-collapsed coordinates in BamWriter; expanded tests accompanied by targeted edge-case scenarios. Representative commits include c6ea97ed28a37f18f70ba8168ad527d41aedec3d, 4ff71f75274dea7882666c70e18986269143f28e, 31beee0b728424c9d46da567586aef834e88df41, a6915199bc24924877f6b711d54904ff2d0605ec, de1e4a2c9638d2d12f7036e81340f8a2169ce188, cca4b3a047e01188a7f1fbc192b8da0dd4974d1c; (2) PartitionReader fix: only check MATE_CIGAR_ATTRIBUTE when the mate is mapped, preventing errors in paired-read processing (ac5b4976b2048ecd19c0b4450915825602775c10); (3) Redux module upgrade to JUnit 5 with TestGenerator for improved test generation and coverage (7abeea6a8089b1249629174bfc3500f23696be68).
February 2025
18 Commits • 11 Features
Feb 1, 2025February 2025 – hartwigmedical/hmftools monthly highlights Key features delivered: - PartitionReader ReadCache dynamics with Illumina sampling and enhanced logging: dynamically adjust read cache sampling for Illumina reads and log reads with excessive left soft clips to aid debugging. Commits: 2d3011b1c9b4b27c0d541fa0a721da6cf1571c3d; 617c488ade5344893fa690e150a7bbb38c03d99e. - Optimize soft-clipping for non-standard consensus reads: apply soft-clipping only when alignment score improvement exceeds the clipping penalty. Commit: eba6c5a11c40118701fa08b5232d58302bf096c8. - BAM output boundary accuracy with consensus reads: update BAM writer upper bound position based on the consensus read's alignment start when consensus formation is enabled. Commit: ef772ba131e9ab09985c755ba8f5966178be5242. - Centralize alignment score calculation in CigarUtils: introduce and relocate alignment score calculation; include score in data representations. Commits: a498b5dd0afbe6a66f45f773a5abac47c1b58d6d; fb4ded946599c7f5103989404df110875f1f5bbb. - Consolidate ConsensusMarker implementation: move ConsensusMarker into the abstract class and remove SBXConsensusMarker subclass. Commit: 6bbb2716af18221c751cb02854dae9839231eaa1. - Biomodal consensus type enhancements (HIGH_QUAL) and LOW_QUAL relocation: introduce HIGH_QUAL consensus type for biomodal jitter analysis and relocate LOW_QUAL_CUTOFF to a utility class for base calling. Commit: 2c7bb5b7d9e3bc11dd413fac6449ae46f616ec72. - Detect and auto-correct swapped R1/R2 FASTQ files in biomodal collapse: analyze first 10k FASTQ pairs to detect swapped order and re-initialize readers if needed. Commits: c9725339195ffa8859ad53964ec1f7abebff9d12; fa6a6cd62136a70542c461bbbdcbabe9c694e2f6. - MSI jitter architecture and consensus integration: refactor MSI jitter integration, align sequencing types with consensus types, and improve jitter plotting with consensus awareness; include cleanup. Commits: 1e08de1cea96cceb8fc86f201a4c497209384be3; 9b6222d91c1aca61c7a3a94e66163fa869ad7d04; 5074fafb1a0663d6686f03e1d7121d5f06037594; 6c43919d2fc507d5810d15674141<seg_2>; 897d837f944366c5d26c06cd632922b2234387d8. - Memory optimization for MicrosatelliteSiteAnalyser: store frequencies of read repeat lengths and reconstruct lists to reduce memory usage. Commit: d519a9313bb2670fed45898a4e143cc33d72e77e. - Illumina BAM utilities for read-name parsing: add IlluminaBamUtils to parse instrument, run, flowcell, and coordinates from read names with robust error handling. Commit: 38e3da337c5cb989ef6fadec3dbbfd14d17b1b66. - PCR cluster counting in Illumina duplicate groups: count PCR clusters within Illumina duplicates and store in consensus read attributes. Commit: 4b97a5a2f33c795ad059344bd45339286a385de4. Major bugs fixed: - Enhanced logging for debugging and issue reproduction. - BAM upper bound calculation fixed for consensus reads. - Soft-clipping logic tightened to avoid non-beneficial clipping. - Reduced memory footprint in MicrosatelliteSiteAnalyser. - Auto-detection of swapped R1/R2 in biomodal collapse to prevent data misalignment. - Robust Illumina read-name parsing with error handling. Overall impact and accomplishments: - Substantial improvements in alignment precision, data integrity, and debugging efficiency across Illumina and biomodal workflows. - Improved performance and memory efficiency, enabling larger-scale analyses with stable jitter and consensus pipelines. - Streamlined maintenance via centralized utilities and removal of redundant classes, leading to a cleaner, more extensible codebase. Technologies/skills demonstrated: - CigarUtils and alignment scoring centralization; enhanced data representations. - BAM writing and Illumina read-name parsing utilities. - Biomodal jitter architecture and consensus-type integration. - Memory optimization patterns and robust error handling for large-scale genomic data processing. - End-to-end data integrity improvements in read extraction, consensus formation, and duplication handling.
18 Commits • 11 Features
Feb 1, 2025February 2025 – hartwigmedical/hmftools monthly highlights Key features delivered: - PartitionReader ReadCache dynamics with Illumina sampling and enhanced logging: dynamically adjust read cache sampling for Illumina reads and log reads with excessive left soft clips to aid debugging. Commits: 2d3011b1c9b4b27c0d541fa0a721da6cf1571c3d; 617c488ade5344893fa690e150a7bbb38c03d99e. - Optimize soft-clipping for non-standard consensus reads: apply soft-clipping only when alignment score improvement exceeds the clipping penalty. Commit: eba6c5a11c40118701fa08b5232d58302bf096c8. - BAM output boundary accuracy with consensus reads: update BAM writer upper bound position based on the consensus read's alignment start when consensus formation is enabled. Commit: ef772ba131e9ab09985c755ba8f5966178be5242. - Centralize alignment score calculation in CigarUtils: introduce and relocate alignment score calculation; include score in data representations. Commits: a498b5dd0afbe6a66f45f773a5abac47c1b58d6d; fb4ded946599c7f5103989404df110875f1f5bbb. - Consolidate ConsensusMarker implementation: move ConsensusMarker into the abstract class and remove SBXConsensusMarker subclass. Commit: 6bbb2716af18221c751cb02854dae9839231eaa1. - Biomodal consensus type enhancements (HIGH_QUAL) and LOW_QUAL relocation: introduce HIGH_QUAL consensus type for biomodal jitter analysis and relocate LOW_QUAL_CUTOFF to a utility class for base calling. Commit: 2c7bb5b7d9e3bc11dd413fac6449ae46f616ec72. - Detect and auto-correct swapped R1/R2 FASTQ files in biomodal collapse: analyze first 10k FASTQ pairs to detect swapped order and re-initialize readers if needed. Commits: c9725339195ffa8859ad53964ec1f7abebff9d12; fa6a6cd62136a70542c461bbbdcbabe9c694e2f6. - MSI jitter architecture and consensus integration: refactor MSI jitter integration, align sequencing types with consensus types, and improve jitter plotting with consensus awareness; include cleanup. Commits: 1e08de1cea96cceb8fc86f201a4c497209384be3; 9b6222d91c1aca61c7a3a94e66163fa869ad7d04; 5074fafb1a0663d6686f03e1d7121d5f06037594; 6c43919d2fc507d5810d15674141<seg_2>; 897d837f944366c5d26c06cd632922b2234387d8. - Memory optimization for MicrosatelliteSiteAnalyser: store frequencies of read repeat lengths and reconstruct lists to reduce memory usage. Commit: d519a9313bb2670fed45898a4e143cc33d72e77e. - Illumina BAM utilities for read-name parsing: add IlluminaBamUtils to parse instrument, run, flowcell, and coordinates from read names with robust error handling. Commit: 38e3da337c5cb989ef6fadec3dbbfd14d17b1b66. - PCR cluster counting in Illumina duplicate groups: count PCR clusters within Illumina duplicates and store in consensus read attributes. Commit: 4b97a5a2f33c795ad059344bd45339286a385de4. Major bugs fixed: - Enhanced logging for debugging and issue reproduction. - BAM upper bound calculation fixed for consensus reads. - Soft-clipping logic tightened to avoid non-beneficial clipping. - Reduced memory footprint in MicrosatelliteSiteAnalyser. - Auto-detection of swapped R1/R2 in biomodal collapse to prevent data misalignment. - Robust Illumina read-name parsing with error handling. Overall impact and accomplishments: - Substantial improvements in alignment precision, data integrity, and debugging efficiency across Illumina and biomodal workflows. - Improved performance and memory efficiency, enabling larger-scale analyses with stable jitter and consensus pipelines. - Streamlined maintenance via centralized utilities and removal of redundant classes, leading to a cleaner, more extensible codebase. Technologies/skills demonstrated: - CigarUtils and alignment scoring centralization; enhanced data representations. - BAM writing and Illumina read-name parsing utilities. - Biomodal jitter architecture and consensus-type integration. - Memory optimization patterns and robust error handling for large-scale genomic data processing. - End-to-end data integrity improvements in read extraction, consensus formation, and duplication handling.
February 2025
January 2025
26 Commits • 16 Features
Jan 1, 20252025-01 Monthly Summary for hartwigmedical/hmftools: Focused performance optimization, consensus-building enhancements, and data-processing improvements across the project. Notable optimizations include Microsatellite analysis optimization (store aggregate counts and reuse a single MicrosatelliteRead per thread) to reduce object churn, implemented in MicrosatelliteSiteAnalyser. Duplicate group collapsing was added for Ultima, Biomodal, and SBX to reduce noise and improve caller precision. SBX reads postprocessing now replaces zero-quality matches with the reference, improving downstream accuracy. Consensus-building enhancements were implemented for SBX and Biomodal, including non-standard consensus improvements and alignment/building refinements, with targeted fixes for alignment start issues. A cached reference genome was adopted across Redux and SBX paths to boost performance. Several bug fixes improved stability and correctness (untrimmed bases adjacent to deleted indels treated as zero quality; reverting SBX consensus base-building changes while keeping necessary SBX logic; alignment start fixes for consensus reads; avoiding null propagation in NonStandardBaseBuilder; and SBX mapQ handling adjustments). This work demonstrates advanced performance engineering (thread-local object reuse, caching), algorithmic improvements in consensus and data processing, and code-quality hardening, delivering higher throughput, more accurate analyses, and more reliable clinical workflows.
January 2025
26 Commits • 16 Features
Jan 1, 20252025-01 Monthly Summary for hartwigmedical/hmftools: Focused performance optimization, consensus-building enhancements, and data-processing improvements across the project. Notable optimizations include Microsatellite analysis optimization (store aggregate counts and reuse a single MicrosatelliteRead per thread) to reduce object churn, implemented in MicrosatelliteSiteAnalyser. Duplicate group collapsing was added for Ultima, Biomodal, and SBX to reduce noise and improve caller precision. SBX reads postprocessing now replaces zero-quality matches with the reference, improving downstream accuracy. Consensus-building enhancements were implemented for SBX and Biomodal, including non-standard consensus improvements and alignment/building refinements, with targeted fixes for alignment start issues. A cached reference genome was adopted across Redux and SBX paths to boost performance. Several bug fixes improved stability and correctness (untrimmed bases adjacent to deleted indels treated as zero quality; reverting SBX consensus base-building changes while keeping necessary SBX logic; alignment start fixes for consensus reads; avoiding null propagation in NonStandardBaseBuilder; and SBX mapQ handling adjustments). This work demonstrates advanced performance engineering (thread-local object reuse, caching), algorithmic improvements in consensus and data processing, and code-quality hardening, delivering higher throughput, more accurate analyses, and more reliable clinical workflows.
December 2024
5 Commits • 2 Features
Dec 1, 2024December 2024 performance summary for hartwigmedical/hmftools: Delivered SBX sequencing support and data handling, enhanced robustness for unpaired reads, and added end-to-end tag propagation utilities. These changes improved data quality and reliability for downstream analyses, validated by targeted tests and code refactors. Key results include configurable SBX base handling, duplex indel preprocessing, improved read pairing logic, and the CopyFastqTags tool.
5 Commits • 2 Features
Dec 1, 2024December 2024 performance summary for hartwigmedical/hmftools: Delivered SBX sequencing support and data handling, enhanced robustness for unpaired reads, and added end-to-end tag propagation utilities. These changes improved data quality and reliability for downstream analyses, validated by targeted tests and code refactors. Key results include configurable SBX base handling, duplex indel preprocessing, improved read pairing logic, and the CopyFastqTags tool.
December 2024
November 2024
5 Commits • 2 Features
Nov 1, 2024In 2024-11, delivered targeted analytics enhancements and a major refactor to hmftools, focusing on stronger analytical capability and code maintainability. Implemented MS jitter analysis by consensus type with SBX-specific handling, enabling more granular microsatellite jitter insights. Completed internal refactor of biomodal collapse, moving the component from bam-tools to fastq-tools and applying cleanup for improved modularity and clearer code organization. Fixed a data-path issue by removing support for writing/tracking reads with cutPoint <= 0 in biomodal collapse, simplifying the workflow and reducing edge-case risk. These changes drive better business value through richer analytics, reduced maintenance burden, and a clearer path for future feature delivery.
November 2024
5 Commits • 2 Features
Nov 1, 2024In 2024-11, delivered targeted analytics enhancements and a major refactor to hmftools, focusing on stronger analytical capability and code maintainability. Implemented MS jitter analysis by consensus type with SBX-specific handling, enabling more granular microsatellite jitter insights. Completed internal refactor of biomodal collapse, moving the component from bam-tools to fastq-tools and applying cleanup for improved modularity and clearer code organization. Fixed a data-path issue by removing support for writing/tracking reads with cutPoint <= 0 in biomodal collapse, simplifying the workflow and reducing edge-case risk. These changes drive better business value through richer analytics, reduced maintenance burden, and a clearer path for future feature delivery.
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Quality Metrics
Correctness86.6%
Maintainability86.6%
Architecture83.0%
Performance77.0%
AI Usage20.0%
Skills & Technologies
Programming Languages
C++JavaKotlinPythonRText
Technical Skills
Algorithm DesignAlgorithm ImplementationAlgorithm ImprovementAlgorithm OptimizationBAM File ProcessingBAM ProcessingBAM processingBackend DevelopmentBioinformaticsBug FixingBuild ManagementCachingCallable InterfaceCode CleanupCode Commenting
Repositories Contributed To
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