Add large-file performance benchmark harnesses and analysis - #30
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Adds the real-code benchmark suite used to profile the validation, preview, and indexed-file paths on synthetic files up to ~1M records, plus the competitive comparison against the VS Code alternatives and the weakness deep-dive. All harnesses drive the actual production code (server/src validators, the VCF field parsers, @gmod/bam), unlike the prior raw-I/O stress_test.py. - bench harnesses: validator sweep, parseVcfHeader before/after, BAM indexed query vs whole-file, BAM coverage depth, GFF3 flat vs hierarchical, population-VCF sample parsing, and TextMate tokenization. - Figure generators (matplotlib) and rendered figures. - ANALYSIS, COMPARISON, and REMEDIATION writeups. These are analysis artifacts under test/stress/, not shipped in the extension.
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Summary
Adds the benchmark + analysis bundle produced while profiling BioFmt on large files. Everything drives the actual production code (validators from
server/src/validators, the VCF field parsers, and@gmod/bam), so the numbers reflect real behavior — unlike the prior raw-I/Ostress_test.py.Contents (all under
test/stress/)parseVcfHeaderbefore/after, BAM indexed-query vs whole-file, BAM coverage-depth, GFF3 flat-vs-hierarchical, population-VCF sample parsing, and TextMate tokenization (BioFmt vs bioSyntax grammars).plot_*.py) + rendered figures (figures/).ANALYSIS.md(performance),COMPARISON.md(vs the 3 VS Code extensions),REMEDIATION.md(prioritized weakness fixes — W4 is addressed in Parse only visible VCF sample columns in the preview #29).Reproduction commands are in
ANALYSIS.md. Not part of the shipped extension bundle.