Open Source Contributor
email: jiefu[dot]zhang1226[at]gmail[dot]com
Education: Bachelor of Physics, Nagoya University, Japan, 2023 - 2027
Ongoing project:
Enhance and develop GeneROOT infrastructure
This project builds on the GeneROOT RNTuple foundation established in GSoC
2025. The work expands the benchmark suite to run reproducibly across heavy
bioinformatics datasets, and introduces cross-format comparisons against
SAM, BAM, and CRAM. On the performance side, it optimizes RNTuple’s
indexing and search by replacing the linear scan in region queries with a
logarithmic binary search, eliminating redundant index structures, and
exposing configurable index granularity. It also evaluates modern genomic
compression schemes (Crumble, QVZ, CALQ, P-block, etc.) for quality-score
data and integrates the most effective candidates. Finally, it brings
RAMtools to feature parity with SAMtools by adding Stat, IdxStats,
FlagStat, View, Split, Merge, and Sort.
Project Proposal: URL
Mentors: Martin Vassilev, Vassil Vassilev, Aaron Jomy
We are partially funded by the
Princeton Department of Physics
and
Princeton Institute for Computational Science and Engineering
(PICSciE).
Contact: David Lange; Vassil Vassilev
This project is supported by the National Science Foundation under Grant OAC-1931408 (2020-2023) and OAC-2311471(2023-2026). Any opinions, findings, conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
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